Winmostar Calculation Manual

Contents




Winmostar
  for Windows

    Vista/7/8/10

Copyrightⓒ X-Ability Co. Ltd.
All Rights Reserved

1. MOPAC

1.1. MOPAC Keywords Setup

Set default value of the keywords required to execute MOPAC computation. Select each box and push [Set]. The value will be listed in the data file.

Hamiltonian ▶ specify Hamiltonian to be used in computation.
AM1 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000,
MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
PM3 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000,
MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
RM1 MOPAC 2007
AM1 EXTERNAL = RM1.rm1 MOPAC 7.1, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
PM5 MOPAC 2002, MOPAC 2006
PM6 MOPAC 2007, MOPAC 2009, MOPAC 2012
PM7 MOPAC 2012
MINDO/3 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000,
MOPAC 2002, MOPAC 2006
MNDO MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000,
MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
MNDO-d MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006,
MOPAC 2009, MOPAC 2012
Method ▶ specify computation method.
EF use EF (Eigen Vector Following) routine for optimization.
TS search transient state with EF.
FORCE calculate vibration frequency
1SCF execute SCF once (no optimization).
IRC no conservation of energy .
IRC=1 calculate intrinsic reaction coordinate; first with normal vibration reversed.
IRC=-1 calculate intrinsic reaction coordinate; first withnormal vibration forward.
Charge set value of electric charge.
Multiplicity specify degree of multiplicity.
OPEN set the numbers of electron and the numbers of orbit in Open-shell calculation.
MM MMOK: use correction of molecular mechanics to CONH bonds.
NOMM: use no correction of molecular mechanicsto CONH bonds
GNORM set threshold value to energy gradient.
LARGE print output as indicated cycle intervals.
GRAPH generate formatted file for viewing molecular orbitals. (GPAGH/GRAPHF)
EXTERNAL read parameters from disk.
STEP specify step size in reaction coordinate.
POINT specify number of points in reaction coordinate.
STEP1/2 specify step size in grid calculation path.
POINT1/2 specify number of points in grid calculation path.
AUX generate AUX file with auxiliary information for the use in other programs.
BONDS print final bond-order matrix.
ENPART specify energy partition into 1 and 2 center components.
ESP calculate Electrostatic potential.
EXCITED optimizeexcited singlet state first.
GEO-OK override the safety check on abnormal distance between atoms.
NOINTER cancel printout of atomic distances.
OLDFPC use fundamental physical constants used in old MOPAC version.
POLAR calculate order of polarization.
PRECISE increase convergence criteria by 100 times.
SYMMETRY impose symmetry or iso-value conditions in the definition of structure.
UHF use unrestricted Hartree-Fock method.
VECTORS print final eigenvectors (wave function)
XYZ do all geometric operations in XYZ (Cartesian) coordinates
Others enter other keywords
Default Keywords ▶
Load read settings from file.
Save save settings.
Reset reset all settings.
Set fix all settings.
Cancel exit without change.


1.2. MOPAC Import

1.2.1. MO (mgf)

Display molecular orbitals image based on MOPAC output.

MOPAC MO Plot
[File]-[Open] open a cube file by selecting via a file open dialog.
[File]-[Exit] close this window.
Save Cube whether to save Cube files while drawing MOs.
Mesh draw iso-energy shell of molecular orbitals with grid mesh.
Contour Map draw iso-energy shell of molecular orbitals with solid model.
Transparency set transparency (0:;opaque to 1:trancparent)
Number of MO set orbital number to be displayed. (HOMO# and LUMO# are shown above the orbit)
Iso Level define the value of iso-surface of probability density of electron(1/A^3)
Energy display energy level diagram.
Points set the number of grid points on a side
Scale set the scale factor for viewing area (default=1.5)
3D use 3D Viewer.
2D display in the molecule window using mesh grid.
VRML use VRML. (VRML viewer must be installed)
Quit close this window.
Jmol output the scripts for Jmol.

Energy Level Diagram
a.u. / eV change units
sliders move origin.
zoom image size (view area)
Quit close window


1.2.2. Charge, Dipole (arc)

Set charges and display a dipole moment from an arc file.



1.2.3. Animation (arc)

Display animated image based on the result of Minimum Energy Path(Reaction Coordinate)calculation by MOPAC.

Animation
slider move frame.
Slow - Fast control speed.
3D anime start 3D Viewer.
Jpeg output a set of JPEG file of animation.
autorew set auto-repeat mode. Replay amimation continuously.
3D start 3D Viewer and set animation window.
Excel write CSV file and open by Excel.
>| ( | ) start / stop animation.
Quit close Animation window.


1.2.4. IRC, STEP (out)

Display animation based on IRC calculation by MOPAC.
※Refer to MOPAC Animation for the operation menus.



1.2.5. Force (out)

Display the vibration spectrum based on force calculation by MOPAC.

IR Spectrum
Quit close IR Spectrum window.
Displ.F set amplitude for the animation view.
Excel write CSV file and display it with Excel.
Y-Level change scale of Y-axis.
Unit select unit from 1/cm, eV, nm. ( only 1/cm allowed)
Raman select from Raman Activity / Depolar (P) / Depolar (U)
Anim. display animation of defined frequency ( peak).
Vector show vector display of defined frequency (peak).
Scal.F. select scaling factor to correct systematic error.
Width set amplitude of half value width.
X-min set minimum wave number ( wave length) to be displayed.
X-max set maximum wave number ( wave length) to be displayed.
X-rev invert wave-number axis.
IR show IR spectrum.
Rev. invert upside down. (absorption spectrum)


2. CNDO/S

2.1. CNDO/S Keywords Setup

Generate script for CNDO/S computation.

Method specify method (CNDO or INDO)
Multiplicity request calculation on singlet (or triplet) excitation state. SINGLET(TRIPLET)
Basis specify basis function. (SP or SPD)
BONDS request output of bond order.
NOINTER request not to output atomic distance.
SHORT request simple output.
OUTMO request output file for MOLMOL2.
Repul.Integ. specify formula of repulsive integration. 1: Pariser, 2: Ohno, 3: Nishimoto-Mataga, 4:Theoletical.
Nuc.Repul. specify formula of nuclear repulsion. 1: Za * Zb / 1, 2: Za * Zb * γab
PKAPPA specify K value for p electron. default = 0.585
DKAPPA specify K value for d electron. default = 0.3
CHARGE specify electric charge.
CI specify the number of excitation states to be included in CI calculation. (upper limit 500)
No. of Excited specify the number of excitation states to be included in output.
Set set parameters.
Cancel exit without modification.
Atoms and coordinates automatically generated by Winmostar.


2.2. UV-VIS Spectrum

Display theoretical peak position and intensity of UV/VIS spectrum based on Gaussian, CNDO/S and MOSF calculation.
※Refer to MOPAC IR Spectrum for the operation menus.



3. GAMESS

3.1. GAMESS Keywords Setup

Set the default value for GAMESS computation, which will be added to the data file.
Select the value of each box and fix with [Set].

$CONTRL ▶
ICHARG define electric charge of the molecule.
MULT specify spin multiplicity.
SCFTYP select type of wave function in SCF calculation.
RUNTYP specify objective of the calculation.
COORD specify data type.
MAXIT specify maximum number of SCF calculations to be repeated.
NZVAR specify the number of internal coordinate.
EXETYP check if you only want to inspect input data.
NOSYM specify symmetry imposed on calculation.
NPRINT specify the extent of detail to be printed out.
LOCAL specify the method of orbital localization. ( default=0:skip localization)
ECP specify Pseudo potential.
DFTTYP specify the type of density function .
TDDFT specify if you need excitation energy calculation with Time-dependent DFT method.
Others set other keywords.
$ZMAT DLC=.T. AUTO=.T. $END NZVAR=3N-6
$SYSTEM ▶
TIMLIM set time limit of calculation. (default=600 min.)
MWORDS set size of memory you need. (default = 1MW)
Others other keywords.
$GUESS ▶
GUESS specify selection of initial orbit.
Others other key words.
$STATPT ▶
NSTEP specify maximum number of steps for optimization.
(default = 20)
OPTTOL set threshold value on energy gradient.
(default = 0.0001 Hartree/Bohr)
METHOD specify algorism for optimization.
HESS specify method for Hessian matrix.
Others other keywords.
$SCF ▶
DIRSCF specify the flag if you need direct SCF.
DAMP use Davidson damping for the Fock matrix.
CONV specify the threshold of SCF density convergence criteria. (default = 1.0D-0.5)
Others other keywords.
$BASIS ▶
Basis Set select wave function to be incorporated in GBASIS, NGAUSS, NDFUNC, NFFUNC, DIFFSP, DIFFS.
GBASIS set of fundamental basis functions.
NGAUSS set number of Gaussian function.
EXTFIL import wave function from external file.
NDFUNC specify the number of heavy-atom polarization functions to be used.
NFFUNC specify the number of heavy-atom f-type polarization functions to be used.
NPFUNC specify the number of heavy-atom p-type polarization functions to be used.
DIFFSP specify if you need sp-diffuse function.
DIFFS specify if you need s-diffuse function.
Others other keywords.
$DFT ▶
LC specify if you need long-range corrected functions.
(only in BLYP, BOP and BVWN)
MU define parameter of long-range corrected functions.
(default= 0.33)
Others other keywords.
$TDDFT ▶
NSTATE set the number of states to be found (excluding ground state).
NRAD set number of radial points in the Euler-MacLaurin quadrature. (default=48)
NLEB set number of angular points in the Lebedev grids. (default=110).
Others other keywords.


3.2. GAMESS Import


3.2.1. Animation

Display animation image based on GAMMES computation.
※Refer to MOPAC Animation for the operation menus.


3.2.2. MO, UV, Charge, Dipole, NMR

Display molecular orbitals and electrostatic charge based on GAMMES computation.
※Refer to MOPAC MO Plot for the operation menus.


3.2.3. Hessian, Raman

Display vibration spectrum based on GAMMES computation.
※Refer to MOPAC IR Spectrum for the operation menus.


3.2.4. RESP charge from punch

Read a punch file and calculate RESP charges.
The punch file must be generated from the run with "GAMESS Keywords>Easy Setup>RESP/ESP".


4. Gaussian

4.1. Gaussian Keywords Setup

Setup a default keyword list for Gaussian computation. Specify each items and [Set] to fix.

LINK0 ▶
#nproc=n specify the number of processor you intend to use.
#Chk=file define check-point file.
#Mem=n set the size of dynamic memory in word unit.You can also use units including KB, MB, GB, KW, MB, GW. (default:6MW)
Comment ▶ describe comments.
# mark the beginning of root section.
#N assign standard printout format (default)
#P assign detailed printout format including time stamps and durations of each links and the information on SCF convergence.
#T assign simple printout format with critical information.
Comment ▶ specify the type of Hamiltonian you intend to use.
hf use Hartree-Fock calculation. In case not explicitly specified, RHF will be used for singlet, and UHF will be used for higher multiplicities.
rhf use restricted Hartree-Fock calculation
uhf use unrestricted Hartree-Fock calculation.
am1 use semi-empilical calculation with AM1 Hamiltonian.
pm3 use semi-empilical calculation with PM3 Hamiltonian.
pm3mm specifies the PM3 model including the optional molecular mechanics correction for HCON linkages.
b3lyp use non-local correlation provided by the LYP expression and Becke3 function.
ub3lyp
mp2 request a Hartree-Fock calculation followed by a Moller-Plesset correlation energy correction truncated at 2nd order.
ump2
mp4 request a Hartree-Fock calculation followed by a Moller-Plesset correlation energy correction truncated at 4th order.
ump4
cis requests calculation on excited states using single-excitation.
cisd requests calculation on excited states using double-excitation. (same as CI)
indo request semi-empirical calculation with INDO Hamiltonian.
cndo request semi-empirical calculation with CNDO Hamiltonian.
gvb request a perfect-pairing General Valence Bond (GVB-PP) calculation.
oniom request a ONIOM calculation.
Basis specify a set of basis function.
Pop ▶ control output including molecular orbitals, orbital energies and atomic charge distribution.
none No orbitals are printed, and no population analysis is done.
minimal Total atomic charges and orbital energies are printed.
regular print five occupied and five virtual orbitals along with the density matrices and a full Mulliken population analysis.
full Same as the above population analysis, except that all orbitals are printed.
Calc. Type ▶ optimize with eigenvalue-following algorithm EF.
opt execute the eigenvalue-following algorithm.
opt=z-matrix perform optimization using internal co-ordinates.
opt=modredundant modify Redundant Internal Coordinates. Input section is required following the structure description.
opt=(ts,noeigentest,calcfc) request optimization of transition state. no distortion test will be done. Force constant will be calculated at the beginning.
irc requests to follow reaction path.
irc=(maxpoint=20, stepsize=20t, calcfc) requests to follow reaction path. Specify the number of points on reaction path and step size.
MaxCyc=n define by n the number of steps for optimization.
Charge define the value of electric charge.
Multi. specify multiplicity.
Freq ▶
freq calculate force constants and the resulting vibrational frequencies.
freq=raman calculate Raman intensities along with IR intensities.
freq=vcd calculate intensity of vibrational circular dichroism (VCD) along with normal frequency analysis.
freq=noraman skip extra steps required to compute the Raman intensities during Hartree-Fock analytic frequency calculations.
freq=nraman calculate derivative function of dipole moment by numerical differentiation of analytical derivative function of dipole with respect to electric field.
freq=nnraman calculate derivative function of polarization by numerical differentiation of analytical derivative function of polalization with respect to nuclear co-ordinates.
Td ▶
td request excited state calculation using the time-dependent Hartree-Fock or DFT method.
td=(nstates=n) calculate td on the states defined by n. (default = 3)
gfinput print current basis set in a same format as input format.
gfprint prints current basis set and density fitting basis set in a same table format as input.
nosym cancel re-orientation and make all computations to be performed in Z-matrix orientation.
guess=read read wave function in the checkpoint file.
geom=check read fragment assignment from checkpoint file.
Others other keywords


4.2. Gaussian Import


4.2.1. Animation

Display animation based on Gaussian computation.
※Refer to MOPAC Animation for the operation menus.


4.2.2. Anim_Opt (IRC, modred)

Display optimized structure given by Gaussian computation.
※Refer to MOPAC Animation for the operation menus.


4.2.3. MO, UV, Charge, Dipole, NMR

Display molecular orbital, UV/Vis spectrum and electrostatic charge based on Gaussian computation.
※Refer to MOPAC MO Plot for the MO operation menus.
※Refer to MOPAC IR Spectrum for the UV-VIS spectrum operation menus.


4.2.4. Freq

Display vibration spectrum based on Gaussian computation.
※Refer to MOPAC IR Spectrum for the operation menus.



4.2.5 Fchk

Generate Cube file from .fch by Cubegen of G03W utility.

Property ▶
MO molecular orbital
Density electron density
ESP spin density
Spin spin density (α - β)
Alpha spin density α
Beta spin density β
Current Density Magnitude of the magnetically-induced current density
Shield Density Magnetic shielding density
Type define the option of Density keyword. (HF, MP2, CI, QCI)
Cube export Cube file.

※Refer to MOPAC MO Plot for the other operation menus.



4.2.6. Cube

Read and visualize Cube files.

Refer open a "File open" dialog and read a cube file.
Map ▶
refer open [file] dialogue and read 2nd cube file for mapping.
map execute mapping on the data indicated above column with the data indicated below column. e.g. map ESP data on Density data.
subtract on the difference between the two cube files.
sub 2 on the square difference between the cube files.
add on the sum of the two cube files.
Cube export the calculation result of cube files employed in mapping [Map] for viewing.
Cubegen execute Cubegen, read .fch file to generate Cube file.
(same as [Import chk])

※Refer to MOPAC MO Plot for the other operation menus.



5. NWChem

5.1. NWChem Keywords Setup

Set the default value for NWChem computation, which will be added to the data file.
Select the value of each box and fix with [Set].

Title set a title
Basis specify a basis set.
Task specify theory and operation.
DFT ▶
Multiplicity specify DFT spin multiplicity.
Exchange specify a DFT exchange functional.
Correlation specify a DFT correlation functional.
SCF ▶
Multiplicity specify SCF spin multiplicity.
Wave Function specify SCF theory.
Property ▶
Mulliken output Mulliken charge.
Shielding compute NMR.
Dipole output dipole moment.
Other settings describe other settings.
MPI processes specify the number of MPI processes.


5.2. NWChem Import


5.2.1. Animation

Display animation image based on NWChem computation.
# Refer to MOPAC Animation for the operation menus.

5.2.2. MO, Charge, Dipole

3Display molecular orbitals and electrostatic charge based on NWChem computation.
# Refer to MOPAC MO Plot for the operation menus.

5.2.3. Frequencies, Raman

Display frequencies and raman spectrum based on NWChem computation.



6. PIO

Set PIO (paired interacting orbitals) analysis by Gaussian/GAMESS.

Set assign the fragments. Click A and then click B. fix by [Set].
Reset reset the assignment of fragments.
Save export data file for combined system A-B and fragment A and B.
Edit edit data file.
Gauss/GAMESS execute Gaussian/GAMESS computation.
GenG generate batch file.
GenP generate data file for PIO.
PIO execute PIO calculation.
ISPC ▶ define the number of peaks to be shown in the diagram. Wave length and intensity will be shown from the longest end.
= 0 generate PIO with all molecular orbitals of both A and B fragments.
= 1 generate PIO with occupied molecular orbital of both A and B fragments, expressing overlap repulsion and closed-shell repulsion between both fragments.
= 2 generate PIO only with occupied orbit of fragment A with empty orbit of fragment B, expressing electron delocalization from A to B.
= 3 generate PIO only with empty orbit of fragment A with occupied orbit of fragment B, expressing electron delocalization from B to A.
Reverse-A / Reverse-B
Edit edit output file of PIO (*.out).
Sum. show summary.
Edit edit output file of PIO (*.log).
MO open command window for viewing molecular orbitals.
Quit close this window.

※Refer to MOPAC MO Plot for the MO plot operation menus.



7. Building simulation cells

7.1. Solvate/Build Cell

Build a simulation cell for a full-atom or ab initio MD simulation.

[Put the molecule on main window as solute] Whether or not to put the molecule on the main window as "Solute" molecule.
[Add Water] Add water molecules.
[Add .mol2 File] Add the molecule written in a mol2 file.
[Delete] Delete the molecule selected at the above list
Simulation Cell▶
[Set Density] Specify the density.
[Set Distance from Solute] Specify the distance from the "Solute" molecule and the simulation cell
[Set Box Size] Specify the box size directly.
[Box Type] The box type.
Option▶
[Water Model] The water model added by [Add Water] button.
[Reset] Reset the settings.
[Build] Build the simulation cell using cygwin.

7.2. Generate Ions

Replace water molecules with mono-atomic ions by using gmx genion. See Gromacs manual for more details.

[Neutral] Neutralize the system.
[Concentration] The concentration for Ions.
[Cations]/[Anions] The name of ions.
[Number of Cations]/[Number of Anions] The number of ions.
[Execute] Execute gmx genion on Cygwin.

8. Gromacs

8.1. Gromacs Keywords Setup

Specify the conditions for Gromacs. Click "OK" after fixing the each items.

Parameters(1) panel
Extending Simulation Whether or not to extend the simulation from the output of the previous run.
Velocity Generation
gen-vel Whether or not to generate the atomic velocities at the first time.
Run control
integrator The calculation algorithm.
Simulation Time
dt The time step for integration.
nsteps The maximum number of the time steps.
Energy Minimization
emtol The tolerance for forces in an energy minimization run.
emstep Initial step size for an energy minimization run.
Boundary Condition
pbc The boundary condition.
Electrostatics
coulombtype The type of the Coulomb potential calculation.
rcoulomb The cutoff radius for Coulomb potential.
VdW
vdwtype The type of the van der Waals (vdW) potential calculation.
rvdw-switch Where to start switching in vdW potential.
rvdw The cutoff radius for vdW potential.
Temperature Coupling
tcoupl The algorithm to control the temperature.
tc-grps The target group for a temperature control.
tau-t The time constant for a temperature control.
ref-t The reference temperature.
Pressure Coupling
pcoupl The algorithm to a control the pressure.
tau-p The time constant for a pressure control.
compressibility specify compressibility for pressure control.
ref-p The reference pressure.
Constraints
constraints The type for constraints.
constraint-algorithm The algorithms for constraints.
Output Control
nstxout The frequency to write atomic coordinates.
nstvout The frequency to write atomic velocities.
nstenergy The frequency to write statistics including energies into edr file (energy file).
nstxout-compressed The frequency to write atomic coordinate with highly-compressed(xtc) format.
Parameters(2) panel  
Neighbor Searching
nstlist The frequency to update the neighbor list.
ns-type The algorithm for the neighbor searching.
cutoff-scheme The scheme of a cutoff for the neighbor searching.
Use buffer-tolerance Whether or not to set the cutoff radius for the neighbor searching automatically.
rlist The cutoff radius for the neighbor list.
Options for Ewald/PME/PPPM
fourier-nx, ny, nz The cutoff radius or number of meshes in wave space for Ewald, PME or PPPM method.
ewald-rtol The tolerance parameter for Ewald, PME or PPPM method.
pme-order The interpolation order for PME method.
Long Range Dispersion Correction
DispCorr Whether or not to use the long range correction for the dispersion potential.
Options for Constraints
lincs-order The highest order in the expansion of the constraint coupling matrix for LINCS method.
lincs-iter The number of iterations for LINCS method.
continuation Whether or not to constrain the distances at the first step.
shake-tol The tolerance for SHAKE method.
Misc.
define -DFLEXIBLE Whether or not to use the flexible water model instead of the rigid water models.
define -DPOSRES Whether or not to enable the position restraints by including posres.itp.
print-nose-hoover-chain-variables Whether or not to carry over the variables for temperature and/or pressure coupling for the future job.
Other Parameters The other settings for mdp file.
Options panel
mdrun ▶
# of MPI Procs (for Remote Job) The number of MPI processes, only for Remote Job Submission.
# of Threads (for Local Job) The number of threads, only for local job.
Verbose Output Whether or not to calculate and display simulation step and remaining time on-the-fly.
maxwarn The maximum number of warning allowed. (0:stop more than one warning message)
Backup Working Directory Whether or not to take a backup of the working directory.
aaa_gmx_tmp folder will be renamed as aaa_gmx_tmp0, aaa_gmx_tmp1, aaa_gmx_tmp2 ...
Concatenate .edr and .trr files Whether or not to concatenate .edr and .trr files at the postprocess.
Unwrap Atoms (trjconv -pbc nojump) Whether or not to write unwrapped coordinates into .gro and .trr files.
Enable Double Precision Whether or not to use Gromacs binaries with double precision.
Restore Working Directory Restore the working folder. This is useful when an extending simulation abnormally stops.
Force Field panel  
Generate Parameters Assign the force field parameters to the system on the main window, and generate a top file.
(General) The force field for the molecules other than proteins or water.
Acpype and our original code would be internally used for GAFF or OPLS/AA-L, and Dreiding, respectively.
(Protein) The force field for proteins. The atoms with the residue names defined in PDB or gro file are recognized as protein atoms. gmx pdb2gmx would be internally used.
(Water) The force field for water. This must be identical with the force field specified at [MD]-[Solvate/Build Cell].
Exception Allow to assign LJ parameters for specific molecular species.
Assign Charges Assign charges calculated from acpype.
Use User-defined Charge Assign charges defined at the main window.
Add [position_restraints] Section for selected atoms Whether or not to write [position_restraints] section in a top file for specific molecular species.
Add [position_restraints] Section for Protein Whether or not to write [position_restraints] section in a top file when protein molecules exist.
Dump Now Dump a top file according to the current settings.
Load from Existing File Use the existing topology file to execute Gromacs.
Edit Open the topology file specified.
Generate Simulation Cell Whether or not to create a simulation cell when that is not defined on the main window.
Saving/loading the settings
Load Setting Read saved calculation condition.
Save Setting Save calculation condition.


8.2. Start Gromacs

Run Gromacs.
If the input file is aaa.dat, Gromacs would be executed as followings.

・Save the molecule as aaa.mol2 (for acpype) or aaa.pdb (for pdb2gmx).
・Make a shell script to launch Gromacs.
・Make the working directory aaa_gmx_tmp.
・Copy the input file and the script to the working directory.
・Run the script.
・The standard output is redirected to aaa.out file in the same directory of the input file.


8.3. Import GRO

Import the coordinates of atoms and the calculation box from a GRO file or a PDB file.
gmx_tmp_mdrun.gro file in the working directory is selected by default.
The name of the opening file is not changed after the import.


8.4. Import Trajectory

Import the coordinates of trajectory from a dump file which is generated by gmxdump from a TRR file.
gmx_tmp_mdrun_trr.dump file in the working directory is selected by default.
The name of the opening file is not changed after the import.
# Refer to MOPAC Animation for the operation menus.


8.5. Energy Plot

Display energy graph from calculation result .edr file.


8.6. Radial Distribution Function

Display graph of radial diffusion function computed by simulation result.
Specify each item and click [OK].

RDF▶  
Reference Group set group to compute radial diffusion function.
Group set opponent group to compute radial diffusion function.
Definition▶
[Atom] set atom coordinate for calculation target.
[center of geometry] set molecule's geometric mean coordinate for calculation target.
[center of mass] move calculation target to position of center of gravity of molecule.
Create Group make new group by selecting specific atoms belonging to some molecular group.
First Frame set initial time as a ps unit for calculation of radial diffusion function.
Output▶
[RDF] compute radial diffusion function.
[Cumulative Number RDF] compute accumulated coordination number.
Draw draw graph of computed result.
Close close calculation window of radial diffusion function.
Autoscale uncheck when clarifying vertical/horizontal axis of graph.
XMIN, XMAX set max/min of horizontal axis of graph.
YMIN, YMAX set max/min of vertical axis of graph.
Redraw redraw graph when setting XMIN, XMAX, YMIN, and YMAX.
Save as CSV save data of displayed graph as csv file.


8.7. Mean-square Displacement

Display graph after calculating mean square displacement from simulation result and calculate self diffusion coefficient.

MSD▶  
Group set group to calculate mean square displacement.
Create Group click to make new group by selecting specific atoms belonging to a certain group(molecule).
First Frame set initial time as a ps unit for calculation of radial diffusion function.
Draw draw graph of computed result.
Close close calculation window of radial diffusion function.
Autoscale uncheck when clarifying vertical/horizontal axis of graph.
XMIN, XMAX set max/min of horizontal axis of graph.
Redraw redraw graph when setting XMIN, XMAX, YMIN, and YMAX.
Save as CSV save data of displayed graph as csv file.
Diffusion Constant draw self diffusion coefficient using Einstein equation by a graph of mean square displacement.

8.8. RMSD

Draw graph about time change of RMSD(Root Mean Square Deviation) against initial coordinate especially in protein system.

RMSD▶  
Group set group to calculate time change of RMSD. Backbone is default.
Create Group click to make new group.
First Frame set initial time as a ps unit for calculation of RMSD.
Draw draw graph of computed result.
Close close calculation window of RMSD.
Autoscale uncheck when clarifying vertical/horizontal axis of graph.
XMIN, XMAX set max/min of horizontal axis of graph.
YMIN, YMAX set max/min of vertical axis of graph.
Redraw redraw graph when setting XMIN, XMAX, YMIN, and YMAX.
Save as CSV save data of displayed graph as csv file.

8.9. Radius of Gyration

Display graph for time change of Radius of Gyration especially in protein system.

RG▶  
Group set group to calculate time change of Radius of Gyration. Backbone is default.
Create Group click to make new group.
First Frame et initial time as a ps unit for calculation of Radius of Gyration.
Draw draw graph of computed result.
Close close calculation window of Radius of Gyration.
Autoscale uncheck when clarifying vertical/horizontal axis of graph.
XMIN, XMAX set max/min of horizontal axis of graph.
YMIN, YMAX set max/min of vertical axis of graph.
Redraw redraw graph when setting XMIN, XMAX, YMIN, and YMAX.
Save as CSV save data of displayed graph as csv file.

8.10. Scattering Function

Calculate the scattering function by using gmx saxs.


8.11. Solubility/Chi/DPD Parameters

Calculate the cohesive energy from the simulation data for the vapor and liquid phases, and determine the Hildebrand's solubility parameter. The chi and DPD aij parameters can also be computed when two different substances are given at this window.


8.12. Setup ERmod

1) Simulate the following three systems before the free energy calculation, and leave the corresponding *_gmx_tmp folders generated by Gromacs on Winmostar. Only the data at the equilibrated states are needed.
  (A) Solution system (one solute molecule and many solvent molecules)
  (B) Solvent system (many solvent molecules)
  (C) Solute system (one solute molecule)

2) Select "Setup ERmod" menu.

3) Push [Select Folder] button for the solution system, and select the folder for (A).

4) Push [Select Folder] button for the solvent system, and select for (B) as well.

5) For the solute system, push [Select File (xtc, gro or pdb)] and select the xtc, gro or pdb file in the folder for (C).

6) Set the parallelism or detail options at "Option" panel if needed.

7-a) To execute the free energy calculation on the local machine, push [Start] button. ERmod will run after specifying the folder for the output files.

7-b) To execute the free energy calculation on the remote server, push [Close] button and open "MD" > "Remote Job Submission" window. Choose "ermod" for program and push [submit] button. The path for ermod and slvfe must be included in the PATH environment variable on the remote server. After the free energy calculation using ermod and slvfe, you need to push [get] button and obtain the folder for the output files into the Winmostar installation directory.

8) Select "Solvation Free Energy (ERmod)" menu.

See ERmod wiki to learn more about ERmod or install on your remote server.


8.13. Solvation Free Energy (ERmod)

Select the folder for the output files specified at "Setup ERmod" to obtain the solvation free energy.
A unit of energy can be changed at "Unit".
Push [Log] button to read the raw output from ERmod.


8.14. Setup BAR

1) Simulate the solution system including one solute molecule and many solvent molecules with Gromacs on Winmostar before the free energy calculation. This system is referred as the state at λ = 1 which means full coupling. Leave all *_gmx_tmp folders for initial coordinate generation (e.g. insert-molecules), energy minimization, equilibration and product runs.

2) Select "Setup BAR" menu.

3) Specify how you divide states between λ = 0 (no coupling) and λ = 1 (full coupling) at "Integration Path" panel. Enter the coupling coefficients λ for van der Waals and Coulomb potentials at the text boxes besides [Insert] button, and push [Insert] to add a new state. You can also use [Delete] button to delete the selected state.

4) Specify the simulation procedures for each states at "Procedure" panel. The folders prepared at 1) must be listed in proper order using [Add] and/or [Delete] buttons. By default, Winmostar automatically search *_gmx_tmp folders in the Winmostar installation directory. The calculation condition listed at the bottom will be used for the free energy calculation.

5) Push [Start] button. The MD simulations for each states will run after specifying the folder for the output files.

8) Select "Solvation Free Energy (BAR)" menu.


8.15. Solvation Free Energy (BAR)

Select the folder for the output files specified at "Setup BAR" to obtain the solvation free energy.
A unit of energy can be changed at "Unit".
Push [Log] button to read the raw output from ERmod.


9. LAMMPS

9.1. LAMMPS Keyword Setup

Set conditions to start LAMMPS.
Click OK after selecting each items.


LAMMPS input files are generated with setting parameters. Modification of generated input files is possible as you need.
Extending Simulation Whether or not to extend a simulation from the previous run.
In File▶  
Boundary X Y Z Set boundary condition.
Dump Interval Specify frequency to write coordinate into dump file with the number of timesteps.
Output Interval Specify frequency to write energy valiables and etc into log files with the number of timesteps.
Ensemble Specify types of time integrals. Select nvt (canonical ensemble which temperature is constant), npt (ensemble which temp and pressure are constant), nve (micro canonical ensemble which volume and energy are constant) or minimize (energy minimization by CG method).
Temperature Specify the temperature to control systems. (Unit:K)
Timestep Specify step size of time integrals. (Unit:femto second)
# of timestep Specify the maximum number of time integral step.
Velocity Check if initial velocity is needed.
Temperature Set initial temperature. (Unit:K)
Data File▶  
Specify data file Check if files are read with read_data command.
Please refer read_data command in LAMMPS manual.
Auto Set cell size regarding molecular size.
Distance Set distance between molecule and computational cell boundary. (Unit:angstrom)
X Low X High Set X upper limit coordinate and X lower limit coordinate of computational cell boundary. (Unit:angstrom)
Y Low Y High Set Y upper limit coordinate and Y lower limit coordinate of computational cell boundary. (Unit:angstrom)
Z Low Z High Set Z upper limit coordinate and Z lower limit coordinate of computational cell boundary. (Unit:angstrom)
Generate
Save computational condition.▶  
Load Setting Read saved computational conditions.
Save Setting Save computational conditions.


9.2. Start LAMMPS

Run LAMMPS using a newly-generated data file, last snapshot written by a previous run, or existing data file.
Output files would be stored in *_lmp_tmp folder.


9.3. Import Trajectory

Import trajectory coordinate from dump file.
# Please refer an item of MOPAC Animation about menu.


9.4. Energy Plot

Display energy graph from log file of calculation result.


10. Amber

10.1. Amber Keywords Setup

Setup a default keyword list for Amber computation. Specify each items and [Set] to fix.

LEaP ▶
Force Field select the type of force field.
Add Na+ specify whether to add Na+ and the number of it.
Add Cl+ specify whether to add Cl- and the number of it.
Solvate whether to add water.
Box/Octahedron select box type.
Solvent select the type of solvent.
Distance specify the distance between the solute and the box boundary.
Other LEaP Commands describe other LEaP commands.
SANDER ▶
imin whether to do energy minimization.
maxcyc specify the max number of cycles.
ncyc specify the number of cycles for the steepest descent algorithm.
ntb specify boundary condition.
igb
ntpr specify frequency to print energy information.
ntwx specify frequency to print coordinates to the trajectory file.
ntt specify switch for temperature scaling.
gamma_ln specify the collision frequency γ.
tempi specify the initial temperature.
temp0 specify the reference temperature.
nstlim specify the number of MD-steps to be performed.
dt specify the time step.
cut specify the nonbonded cutoff.
Other Settings describe other settings for SANDER.


10.2. Start Amber

Run Amber.
Make a working directory and calculate in the directory.



10.3. Import Restart File

Import the coordinates of atoms from the PDB file converted from restrt file by ambpdb.



10.4. Import Trajectory

Import the coordinates of the trajectory from the PDB files converted from mdcrd file by ptraj.
※Refer to MOPAC Animation for the operation menus.



11. Polymer

11.1. Register Monomer

(1) make molecule for registeration with modeling function of Winmostar.
(2) select [Polymer] -> [Register Monomer] after click Head atom and Tail atom.

Register Monomer
[Head], [Tail] the numbers of selected Head atom and Tail atom are displayed.
[Name] select monomer file name.
[OK] save monomer file and close monomer registration window.
[Cancel] discard setting and close monomer registration window.


11.2. Homo Polymer Builder

make and register homo polymer chain using registered monomer.

Homo Polymer Builder  
[Polymer Name] set file name of polymer chain.
[Degree] set degree of polymerization.
[Monomer List] select monomer.
[Display] display selected monomer in graphics window.
[Delete] delete selected monomer file.

[Tacticity]▶  
[Isotactic] make Isotactic Polymer.
[Syndiotactic] make Syndiotactic Polymer.
[Atactic] make Atactic Polymer.
[Racemo Ratio] set racemo ratio (0



[Head/Tail Configulation]▶  
[Head to Tail] superpose head atom and tail atom of monomer and concatenate them.
[Head to Head] superpose between head/tail atoms of monomer and concatenate them.
[Build] start making polymer chain.
[Close] close window.


11.3. Block Polymer Builder

make block polymer chain using registered monomer and register that.

Block Polymer Builder  
[Polymer Name] set file name of polymer chain.
[Degree] set degree of polymerization.
[First Monomer] select head monomer from monomer list.
[Last Monomer] select tail monomer from monomer list.



Internal Monomer  
[Internal Monomer] select internal monomer from monomer list. Put the number of monomer into [Number].
[Number] set the number of internal monomer.
[Add] put the number and the name of setting internal monomer into Internal Monomer List.
[Display] display setting internal monomer in graphics window.
[Delete wmo File] delete setting monomer file.
[Delete From List] delete internal monomer selected in the list from the list.
[Build] start making polymer chain.
[Close] close window.

11.4. Random Polymer Builder

make random polymer chain from registered monomer and register that.

Random Polymer Builder  
[Polymer Name] set file name of making polymer chain.
[Degree] set degree of polymerization.
[First Monomer] select head monomer from monomer list.
[Last Monomer] select tail monomer from monomer list.

Internal Monomer  
[Internal Monomer] selcet internal monomer from monomer list. Put the number of monomer into [Number].
[Ratio] set incidental ratio (0
[Add] put the name and the incidental ratio of setting internal monomer into Internal Monomer List.
[Display] display selected internal monomer in graphics window.
[Delete wmo File] delete setting monomer file.
[Sum of Ration] display sum of Ratio listed in Internal Monomer List.
[Delete From List] delete internal monomer selected in Internal Monomer List.

[Definition of Ratio]▶  
[Probability of Each Monomer] Generate internal monomer in accordance with incidental ratio [Add]. The final ratio of internal monomer is not always coincident with incidental ratio.
[Proportion in Total Monomers] The ratio of finally generated internal monomer is proportional to incidental ratio [Add].
[Build] start making polymer chain.
[Close] close window.

11.5. Polymer Cell Builder

make polymer cell using registered polymer chain.

[Box Configulation]  
[Density] set density.
[X-Axis Length] set angstrom unit of x length of rectangular cell and display that.
[Y-Axis Length] set angstrom unit of y length of rectangular cell and display that.
[Z-Axis Length] display angstrom unit of z length of rectangular cell.
[Cubic Cell] set cubic cell.
[Periodic Boundary Condition]▶  
[X],[Y],[Z] put toggle to the direction of periodic boundary condition.
[Polymer Available]  
[Number] set the number of selecting polymer chain.
[>>Add>>] add selecting polymer chain to Polymers Used List.
[<<Delete<<] delete selecting polymer chain from Polymers Used List.
[Display] display selecting polymer chain in graphics window.
[Delete] delete file of selecting polymer.
[Polymer Used]  
[Build] start making polymer cell.
[Close] close window.

11.6. Settings

specify folder to save files related to polymer builder.

[Polymer Setting]  
[Monomer(*.wmo)Folder] set folder to save monomer file.
[Polymer(*.wpo)Folder] set folder to save polymer chain file.
[OK] save setting and close window.
[Cancel] delete setting and close window.

12. Dissipative Particle Dynamics

12.1. DPD Cell Builder

Create a simulation cell for DPD simulation

[Monomers Available] Select one of the monomers listed here.
[# of Monomers] The number of monomers to be added.
[>> Add >>] Add the selected monomer to the polymer.
[Branch] [Start]Specify where to start a branch.
[End]Specify where to end a branch.
[Monomers Used] The Composition of the polymer.
[Clear] Clear the composition of the polymer.
[<< Delete <<] Delete the selected monomer.
[# of Polymers] The number of polymers to be added.
[>> Add >>] Add the polymers to the system.
[Polymers Used] The list of polymers in the system.
[<< Delete <<] Delete the selected polymer.
[Density] The dimensionless number density of the system.
[Build] Build the simulation cell.
[Reset] Reset the settings on this window.
[Close] Close this window.

12.2. DPD Potential Editor

Create or edit the potential parameters for DPD simulations.

[Potential Files] The list of the potential files for DPD.
[New] Create a new potential file.
[Delete] Delete the selected potential file.
Mass▶
[Mass] The mass (dimensionless)
Bond▶
[R_0] The equilibrium bond length parameter R_0 for a bond potential.
[K] The spring constant parameter K for a bond potential.
Nonbond▶
[Aij] The nonbond potential parameter Aij.
[Rcut] The cutoff length Rcut for nonbond potential.
[OK] Save the settings into the potential files and close this window.
[Close] Discard the settings and close.

13. Interface Builder

13.1. Cell Files

define two concatenating cell information. Click [Next] after setting each item.


Cell 1
[Browse] set concatenating cell files(*.mol2).
[Lattice Constants]
[a],[b],[c],[Alpha],[Beta],[Gamma] display cell constant.

Cell 2
[Browse] set another concatenating cell file(*.mol2).
Lattice Constants
[a],[b],[c],[Alpha],[Beta],[Gamma] display another cell's cell constant.


13.2. Direction


Direction▶
[a-axis] concatenate two cells along with a axis.
[b-axis] concatenate two cells along with b axis.
[c-axis] concatenate two cells along with c axis.


Order▶
[normal] superimpose cell2 on cell1.
[reverse] superimpose cell1 on cell2.
[Adjust Interface] combine surfaces automatically when two surfaces imperfectly matches, if you put check.
[Interval] set cavity width of Joint surface.



13.3. Number

set cell size after concatenation. Start making polymer cell if you click [Build] after setting all items. There are cases which process time becomes longer.


Number of Cell 1
[a-axis] set stack number of cell along with a axis.
[b-axis] set stack number of cell along with b axis.
[c-axis] set stack number of cell along with c axis.

Number of Cell 2
[a-axis] display stack number of cell along with a axis.
[b-axis] display stack number of cell along with b axis.
[c-axis] display stack number of cell along with c axis.

Lattice Constrants
[a],[b],[c],[Alpha],[Beta],[Gamma] display cell constant of the cell after concatenation.
[Build] start making polymer cell. There are cases which process time becomes longer.





14. Crystal Builder

Build Crystals Model

Main menu
[File] Read and save files
[Edit] Edit information of crystal structures
[View] Configure visualizing setting of Crystal Builder
[Tool] Special operation for crystal structures
[File]
[New] Start with a new crystal structure
[Open] Open CIF File
[Save As] Save crystal structures in CIF or XYZ files
[Edit]
[Lattice] Define crystal system、space group、and lattice constants(See 12.2 Basic operation)
[Repeat] Build a super cell
[Exchange Axis] Exchange Axis (a, b, c) and the coordinates of asymmetric unit (x, y, z). See International Tables vol.A for the detail.
[Discard symmetry] Discard space group symmetry and fix the space group as P1. then, all atoms including symmetric unit in the unit cell will be recognized as asymmetric unit.
[Assign Atom] Using the occupancy (_atom_site_occupancy) in the CIF file, randomly generate atoms on each sites. When you want to make supercell according to the occupancy, sufficiently repeat unit cell and use this function.
[View]
[Three View Drawing] Set three view drawing. A camera on the left-up view can rotate, but the others are fixed on a, b and c axes.
Rotation▶ Set rotation mode of camera
[Free] Free rotation
[a axis] Rotate around a axis.
[b axis] rotate around b axis.
[c axis] rotate around c axis.
[Element] Display elements
[Display Bond] Display bonds
[Mesh for Replicated Atom] Visualize symmetric units as mesh
[Display Replicated Atom on Boundary] Display Replicated Atom on Boundary
[Display Unit Cell] Display Unit Cell
[Tool]
[Cleave plane] Switch to cleave plane mode. See 12.3 cleave plane
[Insert vacuum] Switch to insert vacuum mode. See 12.4 insert vacuum

14.2. Basic operation

Define crystal system、space group, lattice constants, and set coordinates of atoms.

Lattice
[Crystal System] Select a crystal system
[Space Group] Select a space group from International Tables numbers or Hermann–Mauguin notations
[Lattice Constant] Set lattice constants

Asymmetric Unit
[Add Atom] Add a new atom to asymmetric units
[Remove Atom] Remove a selected atom from asymmetric units
[Atom] Input and change atomic symbol.
[X], [Y], [Z] Set fractional coordinates of atomic sites.

14.3. Cleave plane

Set miller indices of the surface, and redefine the unit cell.

Step 1/2 Cutting
[Cleave Plane] Define miller indices (h k l) of the surface
[Offset] Set position of the surface with relative position(%) between up and down site in the unit cell.
Step 2/2 Transform Unit Cell
Origin When you redefine unit cell, Click an atom on the origin of new unit cell, and click [Set].
Lattice Vector A When you redefine unit cell, Click an atom on the a axis of new unit cell, and click [Set].
Lattice Vector B When you redefine unit cell, Click an atom on the b axis of new unit cell, and click [Set].
Lattice Vector C When you redefine unit cell, Click an atom on the c axis of new unit cell, and click [Set].
Execute Start redefinition. After that, the operation mode will be switch to basic operation of crystal builder.
(See basic operation)

14.4. Insert vacuum

Insert vacuum layer and build a slab model

Insert Vacuum
[Axis] Select a direction of vacuum layer.
[Bulk] Display thickness [Å] of bulk layer(read only)
[Vacuum] Define thickness[Å] of vacuum layer.
[Total Width] Sum of bulk and vacuum layer(read only)
[Automatically shift to center] When this box is checked, the surface structure will be fixed on the center of the extended cell.
When this box is unchecked, Shift will be available.
[Shift] Set position of surface structure in the extended cell. The value in the edit box indicates fractional coordinate of the position of reference plane.
[Reference Plane] Set position of reference plane.
When "Base" is checked, the reference plane will be the bottom of the bulk structure.
When "Center" is checked, the reference plane will be the center of the bulk structure.

15.1. Quantum ESPRESSO Keywords Setup

Specify the conditions for Quantum ESPRESSO (QE). Click "Set" after fixing the each items. The corresponding keywords in the original pw.x or cp.x will appear when you move the pointer onto an each item.
Output Directory▶ Specify how to set the output directory.
 Create Start the simulation from scratch and create a new output directory.
 Continue Continue the simulation from the previous simulation.
 Select... Continue the simulation from the output directory selected at the open dialog.
Preset Select the preset for the simulation conditions.
Use MPI Specify whether or not to use MPI to parallelize QE runs.
Basic▶  
Calculation The task to be performed.
Automatically Set # of Bands Whether or not to set the number of bands to the default value.
# of Bands The number of bands.
K Points The K points to be calculated.
Total Charge The total charge of the system.
No Symmetry Whether or not to consider the symmetry.
# of Steps The number of steps for the relaxation or MD simulation.
Cell Dynamics Specify the type of dynamics for the cell.
Ion Dynamics Specify the type of dynamics for the ions.
Electron Dynamics Specify the type of dynamics for the electrons in a Car-Parrinello simulation.
Automatically convert to primitive cell Whether or not to convert the simulation cell to the corresponding primitive cell.
Advance▶  
Cutoff Energy▶
 Wave Function The cutoff energy for the wave functions.
 Charge Density The cutoff energy for the charge density or potential energy.
Convergence Threshold▶
 SCF(Energy) The threshold for the SCF calculations.
 Relax(Energy) The threshold for the energy in the relaxation run.
 Relax(Force) The threshold for the force in the relaxation run.
Occupations The method for occupations.
Smearing The method for smearing.
degauss The parameter for smearing.
Mixing Beta The mixing factor for SCF calculations.
Mixing Mode The method for mixing.
Variable Cell Axis Select which of the cell parameters should be moved.
vdW Correction The type of the van der Waals correction.
Dynamics▶  
Time Step The time step for the MD run in atomic units.
Temperature The target temperature.
Pressure The target pressure.
Method The method for the MD simulations.
Ion Temp Control The method for the temperature control.
Initial Ion Velocity How to set the initial velocities for the ions.
Ion Temp Tolerance The tolerance for the temperature control for the ions.
Potential Extrapolation The method to extrapolate the potential energies for a Born-Oppenheimer MD run.
Wave Func Extrapolation The method to extrapolate the wave functions for a Born-Oppenheimer MD run.
Initial Electron velocity How to set the initial velocities for the electrons for a Car-Parrinello MD run.
Effective Electron Mass The effective electron mass for a Car-Parrinello MD run.
Electron Mass Cutoff The cutoff value for the effective electron mass for a Car-Parrinello MD run.
Orthogonalization The orthonormalization method for electronic wave.
ESM▶  
Enable ESM Method Whether or not to use the ESM(Effective Screening Medium) method.
Boundary Condition The type of boundary conditions for ESM method.
Electric Field The electronic field for ESM method.
Enable Constant-μ Whether or not to use constant mu algorithm. The initial charge of the whole system will be set to "Total Charge".
Target Fermi Energy The target Fermi energy for a constant mu run.
Enter Relative Potential... Determine the target Fermi energy using the log file at V=0 and the value of the applied voltage.
Options▶  
Verbosity Verbosity for a QE run.
Backup Working Directory Whether or not to make a backup of the output directory.
Generate Simulation Cell Whether or not to create a simulation cell when that is not defined on the main window.
Attributes▶  
Mass▶ Specify the mass for each elements.
 Default Use the standard values.
 Light Set the mass for all elements to unity.
 Manual Set the each values manually.
Pseudo Potential Select the pseudo potential file installed in pseudo directory of QE.
Reload pseudo Files Reload the pseudo potential files from pseudo directory.
Open pseudo Directory... Open pseudo directory on Explorer.

15.2. Start Quantum ESPRESSO

Execute pw.x or cp.x (for a Car-Parrinelo run) as follows. Assumes the input file is named as aaa.pwin.
1) Generate the batch file, aaa.bat.
2) Create the working directory, aaa_qe_data.
3) Run aaa.bat.
The standard output would be redirected to aaa.pwout.

15.3.1. Animation(pwout)

Specify a output file (pwout) from a QE run, and obtain the energy change and animation of a relaxation calculation. See MOPAC Animation for more details.

15.3.2. Electron Density

Specify an output directory from a QE run, and obtain the isosurface for the electron density. See MOPAC MO Plot for more details.

15.3.3. Lowdin Charge

Specify an output directory from a QE run, and obtain the Lowdin charges on each atoms.

15.3.4. Potential Energy Distribution

Specify an output directory and log (pwout) file from a QE run, and obtain the potential energy distribution along z-axis.

15.3.5. Band Structure

Specify an output directory and log (pwout) file from a QE run, and obtain the band structure.

15.3.6. Density of States

Specify an output directory and log (pwout) file from a QE run, and obtain the density of states.

15.3.7. Difference Density/Energy (ems1)

Speciify two esm1 files generated from different QE runs using ESM method, and obtain the difference electron density and potential energy distribution.

15.3.8. Animation(pos)

Specify a pos file, and obtain the animation of a MD run. See MOPAC Animation for more details.

15.3.9. Energy Plot(evp)

Specify an evp file, and obtain the time evolutions of the energies, volume and/or temperature.

 Show Fragment ER widnow.
 Fragment ER calculates binding free energy from NAMD MD calculation results

16.1. Fragment ER Window

[Solution] Click [...] button and specify a solution PDB file.
Select ligands for multi ligand system.
The ligands appears on the view.
[Set Core] Click fragment atoms of the initial lingand and click [Set Core] button, the other part is set as core.
[Add] Select new fragment from the combobox and click [Add] button, a ligand with the new fragmnet and the core is added to the final ligand list.
[Configure] Show Fragment ER Configuration Window.
[Check] Check whether all atoms types of core part of all ligands are same or not.
forcefireds files of ligands are generaed at the same time.
[Setup] generate NAMD input files (PDB, PSF files).
[Close] Close Fragment ER window.

16.2. Fragment ER Menus

[File]▶
[New Project] Initialize project
[Open Project] Open project
[Save Project] Save project.
[Save Project As] Save project with another name.
[Close] Close Fragment ER window.
[MD]▶
[NAMD Keywords Setup] Show NAMD Keywords Setup window
[Run NAMD] Run NAMD on local machine.
[Run NAMD On Remote Server] Show Remote Job Submission window for Running NAMD on remote server
[Edit .log File] Open NAMD log file with text editor.
[Energy Plot] Draw energy change graph with NAMD log file.
[Import NAMD Trajectory] Import MD trajectory file。
[Clear NAMD Output Files] Delete files generated by NAMD
Delete RunNAMD.bat, RunNAMD.log, dcd, log, coor, namd, vel, xsc, xst files, etc.
[Analysis]▶
[Calculate Free Energy] Caluculate fre energy.
[Edit .log File] Open free energy log file with text editor.
[Import Result] Import the result of free energy calculaiton.
[Clear Analysis Output Files] Delete files generated by free energy calculation.
Delete RunNAMD.bat, RunNAMD.log, dcd, log, coor, namd, vel, xsc, xst files, etc. Delete FreeEnergy.sh, FreeEnergy.log, calc_PdP_kai2.out, parameters_fe files and refs, soln folders, etc.
[Tools]▶
[Preference] Show Preference window

17.3. Fragment ER Confgiuration

Configure Fragment ER.
Configurations are recorded to the project file.

[Solvation]▶
[Drop water and solvate for In-protein] Select whether the waters are relocated for In-protein system or not.
if not seelcted, waters in the initial solution file are used.
if not seelcted, PBC cell must be set in the initial solution file are used.
[Drop water and solvate for In-aqua] Select whether the waters are relocated for In-aqua system or not.
if not seelcted, waters in the initial solution file are used.
if not seelcted, PBC cell must be set in the initial solution file are used.
[Distance from solute to cell boundary] Specify the distance from the solute to PBC cell.
[Forcefield for Ligands] Select forcefield for ligand.
[N-terminal modification] Select N-terminal modification.
[C-terminal modification] Select C-terminal modification.
[Import trajectory Interval] Specify the interval for trajectory imported.
[ERmod]▶
[# of bins for binding energy] Specify the number of bins for binding energy.
[# of insersions for solute (maxins)] Specify maxins for ERmod.
[# of division of the simulation (engdiv)] Specify engdiv for ERmod.
[# of OpenMP threads (for local run)] Specify the number of OpenMP threasd for ERmod local run.
[# of MPI processes (for remote run)] Specify the number of MPI processes for ERmod remoet run.
[OK] Close the window with saving.
[Cancel] Close the window without saving.

17.4. NAMD Keywords Setup

Setting for NAMD MD Calculation.
The settings are recorded to the project file.
Select the systems to be calculated by checkboxes.

[Conf]▶ input file setting for each NAMD system.
[namdcd] Specify interval for trajectory output.
[numlog] Specify interval for log output.
[temperature] Specify temprature.
Initial temparature for In-protein equilibration.
[timestep] Specify timestep.
[numstep] Specify the number of steps.
[Number of Therad] Specify the number of threads for NAMD run.
[Generate Conf Files] Output NAMD input files(namd files).
[Run] Output NAMD input files and run NAMD on local machine.
[Close] Close the NAMD Keywords Setup window.
[Load Default] Load default setting.
[Save Default] Save current setting as default setting.
[Reset Default] Reset default setting to initial setting.

17.5. Import Result

Show summary of the result。
Show energy distribution graph.
Enable to select the systems to be shown.

[log] Open log file with text editor.
[Excel] Save graph data as CSV file and open it with application.
[Close] Close the window.

17.6. Preference

[NAMD Path] Set NAMD executable file path.
[Protein Topology Path] specify topology filefor protein.
[Protein parameter Path] specify parameter filefor protein.

16.1. FDMNES keywords setting

 Set FDMNES keywords to make input file.
 Input keywords and click [Set] button.

Target Atom Select target atom (Absorber) of XAFS spectrum.
Click and select an atom on the main form of Winmostar, and click [Set Atom] button on FDMNES Setup window.
Edge Select target electron shell of XAFS spectrum.
Range Set range of XAFS spectrum.
Cluster Radius Set cluster radius.
FDMNES repeats unit cell to make super cell. the cluster will be extracted from the super cell.
The lager value gives similar condition to the bulk but the performance of computation will be decreased.
Method Select calculation method.
Convolution Output broadening spectrum using Lorentz function
Calc LDOS Output Local density of states (LDOS) into a file whose tail of filename is "_sd*.txt"
Definition for Energy Set definition of energy range to display XAFS spectrum.

16.2. FDMNES execution

 Execute FDMNES
To install FDMNES, see FDMNES install manual
In the case you save setting file as aaa.fdmnes, related files will be made as follows.
・make shell script (aaa.bat) to execute FDMNES
・execute the script
・standard output will be redirected to aaa.fdmnes.log file which is the same location as input file.
・others, output files (aaa_bav.txt, aaa_conv.txt, aaa_sd*.txt, etc) from FDMNES.

16.3. XAFS spectrum

 Read output file of FDMNES, display the graph of XAFS spectrum.

Settings of calculation job of the programs running on remote UNIX servers.

Profile ▶ select profile from registered profiles.
New open new profile.
Copy copy profile from the profile column.
Rename modify the name of profile; set by [OK]
Delete delete profile from the profile column.
Quit close this window.


detect point group symmetry of the modeled molecule.
 (If the molecule does not include metals, you should "clean" the structure before using this function.)

Start point group analysis and visualize symmetry elements
[Analyze] start point group analysis
[Accuracy] set an analyzing accuracy of point group analysis. The degree of symmetry becomes strict with an increase of accuracy or vice versa.
[Shoenflies] display Shoenflies notation of molecular symmetry.
[i] display inversion center.
[Cn Axis] display list of rotation axes.
[Sn Axis] display list of improper rotation axes.
[Mirror] display list of mirror plane.
[Select] display all symmetry elements selected in the list in graphic window.
[Deselect] do not display all symmetry elements released to be selected in the list in graphic window.
[Select All] select all symmetry elements and draw in graphic window.
[Deselect All] release all selected symmetry elements and do not display in graphic window.

 After point group analysis, following functions will be available.
 (In the case that the point group is not C1)

Symmetrize and conversion of "asymmetric unit <=> symmetric unit"
[Symmetrize] With the information of detected point group symmetry, resolve the distortion of the coordinates.
(distortion : Displacement from complete symmetric structure).
[Show] Symmetric Unit : display symmetric unit
Asymmetric Unit : display asymmetric unit
(When asymmetric unit is displayed, go to GAMESS keywords setting. Then you can make GAMESS input including point group information.)
Text area on right-down part show XYZ coordinates of the molecule.