6.14. MD ‣ Gromacs menu

It is a menu about Gromacs.

Because Winmostar runs Gromacs on the Cygwin environment, in order to use this function, please set up CygwinWM is required.

6.14.1. Asign Force Field

Asign Force Field. The choices vary depending on the type of solver.

Automatically assign parameters

Assign new force field parameters.

(General)

Specify the force field for molecules other than proteins and water molecules. In the case of GAFF, GAFF2 or OPLS/AA-+GAFF, acpype is used, in the case of Dreiding, an in-house program is used, and in the case of UFF, modified OpenBabel is used. The setting of Dreiding is written in: file: polymer/dreiding.lib.txt. See Universal Force Field for more information about UFF.

Exception

For specific molecules, assign the user specified LJ parameters without using the force field selected in (General). In the left column of the subwindow, check the molecule you want to specify the LJ parameter and enter the LJ parameter in the right column.

Note

For example, when you want to allocate LJ parameters to solid phase atoms in a solid-liquid interface system.

(Protein/Ion)

Specify the force field of the protein. At this point, atoms assigned amino acid residue names in PDB and gro format are recognized as proteins. Internally gmx pdb2gmx is used. CygwinWM $GMXDATA/top/amber03.ff/ions.itp is used to determine if it is an ion residue name.

Warning

This function can not be used when reading the molecular structure from a file not including residue name.

(Water)

Specify the force field of the water molecule. You must specify the selected water model with Solvate/Build Cell. Internally we get the parameters from the library of Gromacs topology installed in Cygwin.

Add [position_restraints] for protein

If a protein exists, write information ([position_restraints] section) to constrain the position in the topology file with -POSRES on the Advanced tab. Ignored if protein is absent.

Add [position_restraints] for protein

For the molecule specified by the user, write information ([position_restraints] section) to constrain the position in the topology file with -POSRES on the Advanced tab. For example, when fixing solid phase in solid-liquid interface system.

Add [distance/angle/dihedral_restraints] for selected atoms

For the molecule specified by the user, write information to constrain distance, angle, dihedral angle to topology file by -POSRES on the Advanced tab.

Dump Now

Based on the current settings, generate a topology file.

Note

  • If you want to customize the forcefield information by editing it with a text editor, first save the file containing the forcefield information using Dump Now and edit the top for Gromacs or the data file for LAMMPS with a text editor.

  • Next, for Gromacs, import the gro file at File ‣ Import File (select Discard and import), then at Assign Force Field select :guilabel:` Select Use parameters written in topology file and click the OK button. You will then be asked for the location of the top file, so open the top file you just saved and edited.

  • For LAMMPS, import the data file at File ‣ Import File (select Discard and import), then at Assign Force Field, select Use the parameters written in file opened on :guilabel:`main window and click on the Next > button. Then, Select force field appears. Select the general type of force field to use and click the OK button.

  • Charges are taken from the structure displayed in the main window. If more than one type of charge is set in the main window (for example, if the GAMESS log file is opened and Mulliken charge and Lowdin charge are set), the following order of priority is used: (high priority) User charge > NBO charge > Lowdin charge > ESP charge > Mulliken charge (low priority). When the file is opened and the Mulliken charge and Lowdin charge are set (for example, when the file is opened and the Mulliken charge and Lowdin charge are set), the order of priority is User charge > NBO charge > Lowdin charge > ESP charge > Mulliken charge (low priority).

Use parameters defined in external parameter file (for inorganic system, ReaxFF or DPD)

(For LAMMPS) Select when you want to use inorganic potential, ReaxFF or DPD. After pressing the Next > button, specify the type of force field to be actually used.

Use parameters written in topology file

(For Gromacs) Select to execute MD calculation using the existing top file. The corresponding gro file must be open in the main window.

Use parameters written in file opened on main window

(For LAMMPS) Select to execute MD calculation using the existing data file. The data file to be used must be open in the main window. After pressing the Next > button, specify the type of force field to use.

6.14.2. Configure

Set calculation conditions of Gromacs. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.

See Run Gromacs for the behavior when clicking Run.

Assign Charges Automatically will start automatically if there is a molecule to which no charge is assigned. If no force field is assigned, Asign Force Field will be launched automatically.

Reset button returns to the default state. Save the setting excluding Force Field with Save button. Load the setting saved with Save with the Load button.

Continue Simulation

Execute a continuous job.

For details, see Run Gromacs.

Preset

Specify the preset of the calculation condition. Each preset changes the following keywords.

Minimize
(fast)
NVT
(fast)
NPT
(fast)
NVE
(fast)

dt

0.002

0.002

0.002

nsteps

5000

5000

5000

5000

integrator

steep

md

md

md

gen-vel

yes

no

no

tcoupl

berendsen

berendsen

ref-t

300

300

pcoupl

no

parrinello-rahman

ref-p

1,0

pbc

yes

yes

yes

yes

comm-mode

linear

linear

linear

linear

nstcomm

50

50

50

nh-chain-length

10

10

nsttcouple

-1

-1

nstpcouple

-1

constraints

hbonds

all-bonds

all-bonds

all-bonds

lincs-order

4

4

4

lincs-iter

1

1

1

shake-tol

1e-5

1e-5

1e-5

nstxout

100

100

100

100

nstvout

100

100

100

100

nstenergy

10

10

10

10

buffer-tolerance

5e-3

5e-3

5e-3

5e-3

rvdw

1,0

1,0

1,0

1,0

rvdw-switch

0.9

0.9

0.9

0.9

coulombtype

pme

pme

pme

pme

rcoulomb

1,0

1,0

1,0

1,0

rcoulomb-switch

0.9

0.9

0.9

0.9

fourier-spacing

0.12

0.12

0.12

0.12

pme-order

4

4

4

4

ewald-rtol

1e-5

1e-5

1e-5

1e-5

Enable
double precision

False

False

False

False

-DFLEXIBLE

False

False

False

False

Extend simulation
from full-
precision
trajectory

False

False

False

False

Minimize
(medium)
NVT
(medium)
NPT
(medium)
NVE
(medium)

dt

0.001

0.001

0.001

nsteps

10000

10000

10000

10000

integrator

steep

md

md

md

gen-vel

yes

no

no

tcoupl

berendsen

berendsen

ref-t

300

300

pcoupl

no

parrinello-rahman

ref-p

1,0

pbc

yes

yes

yes

yes

comm-mode

linear

linear

linear

linear

nstcomm

50

50

50

nh-chain-length

10

10

nsttcouple

-1

-1

nstpcouple

-1

constraints

hbonds

hbonds

hbonds

hbonds

lincs-order

4

4

4

lincs-iter

1

1

1

shake-tol

1e-5

1e-5

1e-5

nstxout

200

200

200

200

nstvout

200

200

200

200

nstenergy

20

20

20

20

buffer-tolerance

1e-6

1e-6

1e-6

1e-6

rvdw

1.2

1.2

1.2

1.2

rvdw-switch

1.1

1.1

1.1

1.1

coulombtype

pme

pme

pme

pme

rcoulomb

1.2

1.2

1.2

1.2

rcoulomb-switch

1.1

1.1

1.1

1.1

fourier-spacing

0.11

0.11

0.11

0.11

pme-order

4

4

4

4

ewald-rtol

1e-6

1e-6

1e-6

1e-6

Enable
double precision

True

True

True

True

-DFLEXIBLE

False

False

False

False

Extend simulation
from full-
precision
trajectory

False

False

False

False

Minimize
NVT
NPT
NVE

dt

0.0005

0.0005

0.0005

nsteps

20000

20000

20000

20000

integrator

steep

md

md

md

gen-vel

yes

no

no

tcoupl

nose-hoover

nose-hoover

ref-t

300

300

pcoupl

no

parrinello-rahman

ref-p

1,0

pbc

yes

yes

yes

yes

comm-mode

linear

linear

linear

linear

nstcomm

1

1

1

nh-chain-length

1

1

nsttcouple

1

1

nstpcouple

1

constraints

hbonds

hbonds

hbonds

hbonds

lincs-order

8

8

8

lincs-iter

2

2

2

shake-tol

1e-9

1e-9

1e-9

nstxout

400

400

400

400

nstvout

400

400

400

400

nstenergy

40

40

40

40

buffer-tolerance

1e-9

1e-9

1e-9

1e-9

rvdw

1.5

1.5

1.5

1.5

rvdw-switch

1.4

1.4

1.4

1.4

coulombtype

pme

pme

pme

pme

rcoulomb

1.5

1.5

1.5

1.5

rcoulomb-switch

1.4

1.4

1.4

1.4

fourier-spacing

0.10

0.10

0.10

0.10

pme-order

6

6

6

6

ewald-rtol

1e-9

1e-9

1e-9

1e-9

Enable
double precision

True

True

True

True

-DFLEXIBLE

False

False

False

False

Extend simulation
from full-
precision
trajectory

False

False

False

False

Minimize
(vapor,fast)
NVT
(vapor,fast)
NPT
(vapor,fast)
NVE
(vapor,fast)

dt

0.002

0.002

0.002

nsteps

5000

5000

5000

5000

integrator

steep

md

md

md

gen-vel

yes

no

no

tcoupl

berendsen

berendsen

ref-t

300

300

pcoupl

no

parrinello-rahman

ref-p

1,0

pbc

no

no

no

no

comm-mode

angular

angular

angular

angular

nstcomm

50

50

50

nh-chain-length

10

10

nsttcouple

-1

-1

nstpcouple

-1

constraints

hbonds

all-bonds

all-bonds

all-bonds

lincs-order

4

4

4

lincs-iter

1

1

1

shake-tol

1e-5

1e-5

1e-5

nstxout

100

100

100

100

nstvout

100

100

100

100

nstenergy

10

10

10

10

buffer-tolerance

5e-3

5e-3

5e-3

5e-3

rvdw

1,0

1,0

1,0

1,0

rvdw-switch

0.9

0.9

0.9

0.9

coulombtype

cut-off

cut-off

cut-off

cut-off

rcoulomb

1,0

1,0

1,0

1,0

rcoulomb-switch

0.9

0.9

0.9

0.9

fourier-spacing

pme-order

ewald-rtol

Enable
double precision

False

False

False

False

-DFLEXIBLE

False

False

False

False

Extend simulation
from full-
precision
trajectory

False

False

False

False

Minimize
(vapor)
NVT
(vapor)
NPT
(vapor)
NVE
(vapor)

dt

0.0005

0.0005

0.0005

nsteps

20000

20000

20000

20000

integrator

steep

md

md

md

gen-vel

yes

no

no

tcoupl

nose-hoover

nose-hoover

ref-t

300

300

pcoupl

no

parrinello-rahman

ref-p

1,0

pbc

no

no

no

no

comm-mode

angular

angular

angular

angular

nstcomm

1

1

1

nh-chain-length

1

1

nsttcouple

1

1

nstpcouple

1

constraints

hbonds

hbonds

hbonds

hbonds

lincs-order

8

8

8

lincs-iter

2

2

2

shake-tol

1e-9

1e-9

1e-9

nstxout

400

400

400

400

nstvout

400

400

400

400

nstenergy

40

40

40

40

buffer-tolerance

1e-9

1e-9

1e-9

1e-9

rvdw

1.5

1.5

1.5

1.5

rvdw-switch

1.4

1.4

1.4

1.4

coulombtype

cut-off

cut-off

cut-off

cut-off

rcoulomb

1.5

1.5

1.5

1.5

rcoulomb-switch

1.4

1.4

1.4

1.4

fourier-spacing

pme-order

ewald-rtol

Enable
double precision

True

True

True

True

-DFLEXIBLE

False

False

False

False

Extend simulation
from full-
precision
trajectory

False

False

False

False

Minimize
(NMA)
NMA

dt

nsteps

20000

20000

integrator

l-bfgs

nm

gen-vel

tcoupl

ref-t

pcoupl

ref-p

pbc

yes

yes

comm-mode

nstcomm

nh-chain-length

nsttcouple

nstpcouple

constraints

none

none

lincs-order

lincs-iter

shake-tol

nstxout

400

400

nstvout

400

400

nstenergy

40

40

buffer-tolerance

1e-9

1e-9

rvdw

1.5

1.5

rvdw-switch

1.4

1.4

coulombtype

pme

pme

rcoulomb

1.5

1.5

rcoulomb-switch

1.4

1.4

fourier-spacing

0.10

0.10

pme-order

6

6

ewald-rtol

1e-9

1e-9

Enable
double precision

True

True

emtol

0.01

-DFLEXIBLE

True

True

Extend simulation
from full-
precision
trajectory

False

True

# of Threads

Specify the thread parallel number.

MPI (for Remote Job)

Specify MPI parallel number. It is reflected only when executing by remote job submission.

Basic
Run Control
dt

Specify one step increment in numerical integration.

nsteps

Specify the maximum number of steps to calculate.

integrator

Specify the calculation algorithm.

Velocity Generation
gen-vel

Specify whether to generate the initial speed.

Fix random seed

When checked, gen-seed will be used.

gen-seed

Specify the initial speed random seed.

Explicitly set gen-temp

If checked, I will do the initial speed temperature here. If you do not enter ref - t will be the initial speed temperature.

Temperature Coupling
tcoupl

Select the temperature control algorithm.

tc-grps

Specify the group to be temperature controlled (more than one can be set with a space delimiter).

ref-t

Specify the set temperature (Multiple settings can be set with a space delimiter).

year-t

Specify the time constant for temperature control (more than one can be set with a space delimiter).

Pressure Coupling
pcoupl

Select pressure control algorithm.

pcoupltype

It shows how to move cells in pressure control.

ref-p

Specify set pressure.

year-p

Specify the time constant for pressure control.

compressibility

Specify the compression ratio of the whole system.

Advanced
Boundary Condition
pbc

Select the periodic boundary condition.

Energy Minimization
emtol

Specify the maximum force which is the convergence condition of energy minimization calculation.

emstep

Specify the initial value of step width to move particles in energy minimization calculation.

Run Control
comm-mode

Specify how to remove the momentum of the whole system.

nstcomm

Specify the frequency of removing the momentum of the whole system.

Temperature/Pressure Coupling
nh-chain-length

Specify the number of stages of Nose-Hoover chain when temperature is controlled by the Nose-Hoover method.

nsttcouple

Specify the frequency of temperature control.

nstpcouple

Specify the frequency of temperature control.

refcoord-scaling

Specify the scaling of the reference coordinates of position restraint during temperature control.

Constraints
constraints

Select the constraint condition.

constraint-algorithm

Select the constraint algorithm.

continuation

Specify whether to inherit the constraint distance from the parent job.

lincs-order

Specify the order of the LINCS method.

lincs-iter

Specify the number of iterations in the LINCS method.

shake-tol

Specify the truncation error parameter used for the convergence judgment of the SHAKE method.

Misc.
print-nose-hoover-chain-variables

Specify this parameter when transferring temperature/pressure control parameters to a child job.

define -DFLEXIBLE

Select to make water molecule flexible.

define -DPOSRES

Select this to constrain the position of a specific molecule. (Include posres.itp)

Extend simulation from full-precision trajectory

If this item is checked and Continue Simulation is checked, the job is continued from the trr file of the previous job. If this item is not checked, the job is continued from the gro file in the final state of the previous job. For example, if you want to run normal mode analysis after the energy minimization calculation, you need to check the box.

Output
Output Control
nstxout

Specify the frequency of atomic coordinates output in steps.

nstvout

Specify the frequency of atomic velocity output in steps.

nstenergy

Specify the frequency of outputting system-wide statistics such as energy to edr file (energy file) in steps.

nstxout-compressed

Specify the frequency of atomic coordinates output in xtc format which can save file size by the step number.

compressed-x-grps

Specify the group to output in xtc format. By default, the entire system is targeted.

Interaction
Modify cutoff radii not to exceed L/2

When checked, automatically adjusts rlist, rvdw, rvdw-switch, rcoulomb, and rcoulomb-switch so that they do not exceed half the lattice constant.

Neighbor Searching
nstlist

Specify how often to update the neighbor list.

ns-type

Specify how to create the neighbor list.

cutoff-shceme

Specify the method of selecting atoms to be included in the neighbor list.

Use buffer-tolerance

Specify the truncation error of binary potential energy, which is a parameter for automatically setting the cutoff distance of the neighbor list. When unchecked, the value of rlist is set as the cutoff distance.

rlist

Specify the cutoff distance of the neighbor list.

VdW
vdwtype

Specify the calculation method of van der Waals potential.

rvdw-switch

When Switching is selected for Van der Waals potential calculation, specify the distance at which Switching starts.

rvdw

Specify the cutoff distance of van der Waals potential calculation.

DispCorr

Select whether long-distance correction of energy and pressure accompany cutoff.

vdw-change

Select settings such as Switching/Shift when Van der Waals potential cutoff.

Electrostatics
coulombtype

Specify the calculation method of coulomb potential.

rcoulomb-switch

When Switching is selected for Coulomb Potential Calculation, specify the distance at which Switching starts.

rcoulomb

Specify the real space cutoff distance of Coulomb potential calculation.

Coulomb-change

Select the setting such as Switching/Shift at the cutoff of Coulomb potential.

Ewald
Set # of grids for fourier space

If checked, use fourier-spacing. If you do not want to use it, use fourier-nx, ny, nz.

fourier-spacing

Ewald, PME or PPPM method in wave number space mesh size.

fourier-nx, ny, nz

Ewald, PME or PPPM method to specify the cutoff distance or mesh number (x, y, z component, respectively) of wave number space.

pme-order

Specifies the order of the extrapolation function in the PME method.

ewald-rtol

Ewald, PME or PPPM method accuracy parameters.

Other
Other Parameters

Specify other settings based on the description of the mdp file.

Automatic
Rescale velocities to..

Use it when you want to bring the system temperature closer to the target temperature in the NVE ensemble. Calculate the scaling factor from the average temperature under calculation and the temperature entered here and scale the velocity of each particle in the final structure.

Rescale box size to..

It is used when calculating with the NVE or NVT ensemble in the state close to the set pressure after calculating with the NPT ensemble. Scale the final structure to the average cell size under calculation.

Options
Restore Working Folder

Click to return working folder to its pre-execution status, such as when a continuous job ends abnormally.

Dump .mdp File

Create and save a Gromacs calculation condition (mdp) file with the settings in the currently opened window.

Dump All Files for Remote

This function does not run Gromacs, but only saves the files needed for Gromacs calculations. Please open the Tools ‣ Remote Job Submission window before using this function.

Rerun from xtc

For the structure of the trajectory (xtc) file output from a calculation that has already been completed, only the energy is calculated using the calculation conditions set in the currently opened window, and the energy (edr) file is obtained.

Open top file

Open the top file generated by the Assign Force Field function in a text editor.

maxwarn

Allow continuation of calculation warning message Specify the maximum number of messages (0: suspend with one or more messages)

Verbose Output

Specify this when displaying the step under calculation.

Concatenate .edr and .trr files

Click to merge with the executed .edr file and .trr file. File binding is performed as postprocessing of Continue Simulation.

Unwrap Atoms (trjconv -pbc nojump)

Output the calculated .gro and .trr files at coordinates that do not wrap around at periodic boundaries (unwrapped).

Enable Double Precision

Execute MD calculation and pre-post processing with double precision version of Gromacs binary.

Overwrites any output file without making a backup in working folder

If checked, when creating a new file in the working folder, a backup will be made if there is an old file with the same name. To save disk space, it is recommended to uncheck this item if Make a Backup of Working Folder is checked.

Enable detailed parallelization setting

Instead of using -nt to specify the number of total threads, the number of parallel Thread-MPI (-ntmpi) and OpenMP (-ntomp) threads can be specified individually.

# of Thread-MPI

Specifies the number of Thread-MPI parallel number.

# of OpenMP

Specifies the number of OpenMP parallel number.

Reset

Reset settings..

Import

Loading configuration file.

Export

Output configuration file.

6.14.3. Run Gromacs

Run Gromacs. The execution method differs depending on the situation.

  • (Default) If Continue Simulation is unchecked and Automatically assign parameters is checked on Asign Force Field

    Create a new coordinate file (extension: gro) and topology file (extension: top) before starting the job.

  • If Continue Simulation is unchecked and :guilabel:` Use parameters from topology file` is selected for Asign Force Field

    Start the job using the coordinate file (extension: gro) opened in the main window and the topology file (extension: top) specified at Asign Force Field.

  • When Continue Simulation is checked

    The coordinate file ( gmx_mdrun_tmp.gro) and the topology file ( gmx_tmp.top) in the working folder linked to the coordinate file (extension: gro) ) To start the job.

Following file will be generated with execution. As an example, the file/folder name when the input file is water.gro is also shown.

type

Description

out file
water.out

water.sh standard output text file.

sh file
water.sh
For running Gromacs and its pre/post processing
Shell script.
bat file
water.gro.bat

This is a batch file for executing water.sh.

Working Folder
water_gmx_tmp\
Working folder.

The following files are generated in the working folder. Only the main files are shown here.

type

Description

input.gro
In the case of a new job, the gro file specified at the time of execution is
copied.
In case of continuous job, it becomes the file of the previous job.
gmx_tmp.top
In the case of a new job, the top file specified at the time of execution is
copied.
In case of continuous job, it becomes the file of the previous job.
gmx_tmp.mdp
It is a file that specifies calculation conditions.
gmx_tmp_mdrun.tpr
Generate from gro, top, mdp file
It is an input file of mdrun.
gmx_tmp_mdrun.ndx
Index file for result processing.
gmx_tmp_mdrun.edr
Temperature, pressure, energy etc. were stored
It is an energy file.
gmx_tmp_mdrun.gro
It is a gro file of the final structure.
gmx_tmp_mdrun.trr
It is a trajectory file.
gmx_tmp_mdrun.xtc
Compressed trajectory file.
gmx_tmp_mdrun.log
This is the log file of mdrun.

Hint

** Working folder **

  • A working folder is a folder whose name is the name of the file opened in the main window plus a suffix.

    • ** The suffix varies depending on the type of solver. **

    • For example, in the case of Gromacs, if the file opened in the main window is aaa.gro and the suffix is _ gmx_tmp, the working folder will be named aaa_gmx_tmp .

  • It must be in the same hierarchy as the file opened in the main window.

  • Processing continues in the working folder of the same name even when continuing jobs, but by default the backup of the working directory of the previous job is created just before the continuation job is executed.

    • The name of the backup will be the one with the smallest number in the range where duplicate names do not exist. For example, if the working folder is aaa_gmx_tmp, it is aaa_gmx_tmp1.

    • ** Directories without numbers are always up to date. **

The job is run through Winmostar Job Manager.

6.14.4. Open Log File (log)

Open the log file (* _ gmx_tmp gmx_tmp_mdrun.log) of gmx mdrun with a text editor.

6.14.5. Open Stdout File

Open the standard output (*. Out) of the shell script when running Gromacs with a text editor.

6.14.6. Animation

Select the gro file and trr file, and animate the MD calculation trajectory.

The file name of the main window does not change.

For the animation display operation method, see Animation display area.

6.14.7. Energy Plot

Selects the Gromacs output edr file and displays graphs of various thermodynamic quantities, such as energy, temperature, and pressure. Internally, the command gmx energy is executed. Please refer to the manual of gmx energy for more detailed behavior.

Please see Energy Plot window for how to operate subwindow.

6.14.8. Import Last Coordinate (gro)

* _ gmx_tmp \ gmx_tmp_mdrun.gro.

When using this function, the file name of the main window does not change.

6.14.9. Configure Sequential Job

Configure settings for continuous execution of Gromacs. If you want to run with settings other than the presets, enter the calculation conditions you want to run in advance with Configure and save it in gmxset format with the Save button.

6.14.10. Run Sequential Job

Run Gromacs sequentially based on the contents of Configure Sequential Job.

6.14.11. Analyses

6.14.11.1. Radial Distribution Function

Select a trr, tpr or ndx file output by Gromacs and display the radial distribution function. Internally, the command gmx rdf is executed. Please check the manual of gmx rdf for more detailed behavior. Radial distribution functions are computed between Reference Group and Target Group.

Definition
Atom

Set the calculation target to atomic coordinates.

Center of geometry

Make the calculation target geometric mean coordinates of the molecule.

Center of mass

Make the calculation target the molecular centroid position.

Output
RDF

Calculate radial distribution function.

Cumulative Number RDF

Calculate the integrated coordination number.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.2. Diffusion Constant/Mean Square Displacement

Select the trr, tpr, and ndx files output by Gromacs and display the mean square displacement and self-diffusion coefficient. Internally, the :command gmx msd is executed. Please refer to the manual of gmx msd for more detailed behavior.

Diffusion Constant

Use the gmx msd command to display the self-diffusion coefficient calculated from the slope of the time-mean square displacement graph.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.3. Scattering Function

Select a trr, tpr or ndx file output by Gromacs and display the scattering function. Internally, the :command gmx saxs is executed. Please refer to the manual of gmx saxs for more detailed behavior.

Interval

Specify the interval at which to acquire the snapshot used to calculate the scattering function. Attention is necessary because enormous calculation is necessary if it is too small.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.4. Velocity Autocorr/Vibration Spectrum

Select the trr, tpr, and ndx files output by Gromacs to display the velocity correlation function and the vibration spectrum. Internally, the :command gmx velacc is executed. Please refer to the manual of gmx velacc for more detailed behavior.

Velocity Autocorrelation

Output speed correlation function.

Vibration Spectrum

Output vibration spectrum.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.5. Static Dielectric Constant

Select a trr, tpr or ndx file output by Gromacs to display the distribution and histogram of the relative permittivity or dipole moments. Internally, the :command gmx dipoles is executed. Please refer to the manual of gmx dipoles for more detailed behavior.

Dielectric constant

Plot the relative dielectric constant. The value of epsilon at the last time in the graph is the relative dielectric constant obtained from that calculation. The value is output below the graph.

Histogram of total dipole momen

Plot the distribution of dipole moments for molecules belonging to the Target Group.

Autocorrelation functino of dipole moment

Plot the autocorrelation function of the dipole moments. The definition of a dipole moment is selected in Definition.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.6. Share Viscosity

Select the trr, tpr, ndx file output by Gromacs and display the viscosity. Internally, the :command gmx tcaf is executed. Please refer to the manual of gmx tcaf for more detailed behavior.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.7. Density Profile

Select a trr, tpr or ndx file output by Gromacs to display the density distribution. Internally, the :command gmx density is executed. Please refer to the manual of gmx density for more detailed behavior.

Group

The density distribution is output for the components that are checked here.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.8. Free Volume

Select a trr, tpr or ndx file output by Gromacs to display the density distribution. Internally, the :command gmx freevolume is executed. Please refer to the manual of gmx freevolume for more detailed behavior.

Radius of probe

Specify the radius of the virtual probe particles that are randomly inserted into the system when calculating the free volume.

# of probe insertions

Specify the number of virtual probe particle insertions.

Random seed

Specify a random seed to determine where to insert virtual probe particles.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.9. Hildebrand Solubility Parameter

Calculate the Hildebrand solubility parameter from the edr, gro file output by Gromacs. Calculation results of gas phase and liquid phase are required. Hildebrand The gmx energy command is executed to obtain the cohesion energy, density (specific volume) and compression rate necessary for calculating the solubility parameter.

6.14.11.10. Chi/DPD parameter

Calculate the Chi parameter · DPD aij parameter from the edr, gro file output by Gromacs. It is necessary to calculate the gas phase and liquid phase of each of the two components. Internally use the value calculated by Hildebrand Solubility Parameter.

6.14.11.11. Bond/Angle/Dihedral distribution

Select a trr, tpr, or ndx file output by Gromacs to display the distribution of distances, angles, or two-plane angles between the selected groups. Internally, the gmx distance command (distance) or the gmx angle command (angle, two plane angle) is executed. Please refer to the manuals of gmx distance and gmx angle for more detailed behavior.

vdwtype

Select the type of value to plot (bond, angle, dihedral, improper or ryckaert-bellmemans).

Calculate for marked atoms

Calculates the distance, angle, or dihedral angle between atoms marked with a marker in the main window.

Calculate for target group

Calculate the distance, angle, or dihedral angle using the NDX file selected in the Target Group.

Calculate for

Calculates the angle or dihedral angle for the selected angletype or dihedraltype.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.12. Hydrogen bonding analysis

Selects the trr, tpr, and ndx files output by Gromacs and analyzes the hydrogen bonds between the selected groups. Internally, the gmx hbond command is executed. Please refer to the gmx hbond manual for detailed behavior.

vdwtype

Select the type of values to plot.

Cutoff angle

Specifies the cutoff value for the hydrogen-donor-acceptor angle when determining hydrogen bonding.

Cutoff distance

Specifies the cutoff value for the donor-acceptor distance when determining hydrogen bonding.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.13. Root Mean Square Deviation

Select the trr, tpr, and ndx files output by Gromacs and display the RMSD (mainly for proteins). Internally, the :command gmx rms is executed. Please refer to the manual of gmx rms for more detailed behavior.

Group

Results are output for the components checked here. Normally select Backbone.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.14. Radius of Gyration

Select a trr, tpr or ndx file output by Gromacs and display the rotation radius (mainly for the protein). Internally, the :command gmx gyrate is executed. Please refer to the manual of gmx gyrate for more detailed behavior.

Group

Results are output for the components checked here. Normally you will select Backbone.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.11.15. Ramachandran Plot

Select the trr, tpr, and ndx files output by Gromacs to display the Ramachandran plots for each amino acid residue. Internally, the :command gmx rama is executed. Please refer to the manual of gmx rama for more detailed behavior.

Residue

Here a Ramachandran plot of the selected residue is output.

Target Group

Calculate the physical quantity for molecules/atoms belonging to the selected group here. A group written in the opened ndx file can be selected here.

Reference Group

It only appears for physical quantities to be calculated for atom pairs such as radial distribution functions. The physical quantity is calculated between Target Group and Reference Group.

Create Group

Register a new group from the atom name written in the gro file.

To define atoms group selected in the main window as a group, use MD ‣ Gromacs ‣ Add Selected Group to Index File (ndx).

In the Create Group window, check Extracted Atom Names and enter New group Name and press the Create button, the group is added to the ndx file It will be added. When you press the Close button, the groups added to Target Group and Reference Group are added.

First Frame

Specify the start time when trajectory is read in ps units.

Last Frame

Specify the end time, in ps, to read trajectories. If Maximum is checked, the last frame is specified.

Draw

Execute the result analysis program and display the graph.

For how to operate the graph drawing area, see How to operate the graph.

6.14.12. Modify Trajectory File

You can perform operations such as thinning, rotation, and calculation of spatial distribution functions on the trajectory data in the trr or xtc file output from Gromacs. Internally, the :command gmx trjconv is executed. Please refer to the manual of gmx trjconv for more detailed behavior. Click Execute button to start the process.

Output interval

Specify how many frames to output by thinning the trajectory.

Postprocess

Specify the operation after processing. If Spatial distribution function is selected use gmx spatial.

Target group

Specify the group to output.

Rotate and Trans

The group specified by Reference group is fixed so that the group specified by Target group is rotated and translated.

Reference group

Specify refernce in Roate and Trans.

Group for SDF

Specify which group to calculate SDF calculated when Spatial distribution function (SDF) is selected in Postprocess.

6.14.13. Start ER

Calculate the solvation free energy using the energy indication (ER) method.

  1. Execute the calculation of the following three in Gromacs beforehand and leave each working folder. Only use equilibrium state data after finishing equilibration such as energy minimization.

    1. Solution system (1 solute molecule + many solvent molecules)

    2. Solvent system (large number of solvent molecules)

    3. Solute system (one solute molecule)

  2. Drag and drop the working folder of A. Solution system on the Solution tab. Or, in each column of the xtc, log, top file, press button to read individual files.

  3. Likewise select the B. Solvent system file on the Solvent tab.

  4. Similarly select the C. Solute system file in the Solute tab. If an xtc file is specified, if the solute specifies a flexible model, pdb or gro file, it is treated as a rigid body model.

  5. Select the molecular name of the solute in Solute Name.

  6. If necessary, specify MPI parallel number at free energy calculation from Options button.

  7. To implement free energy calculation in the local environment press the Start button. Calculation begins when you specify the folder to output the result. On Cygwin, ermod flows.

  8. To implement in the remote environment, press the Close button once. And at Remote job execute Program with ermod. On the remote server, it is necessary for ermod and slvfe command to pass $PATH. (Installing ERmod on remote server is here <https://winmostar.com/en/gmx4wm_en_linux.html>) After finishing the calculation, press get button in Remote job, you will find ermod_remote_* under the folder where winmostar.exe is placed and the result is transferred from the remote server.

  9. After calculating the free energy calculation, to display the result, select the Import ER menu.

Hint

If you want to analyze the data using ERmod functions, which are not supported by Winmostar, you can also follow the procedure below.

  1. First, we will use Winmostar to calculate the MD for solution, solvent only, and solute only. For those procedures, please refer to the tutorial on using the ER method.

  2. Follow the steps after “Generate input configuration for running ermod” in Quick Start Guide on the official ERmod homepage. Follow the steps after “Generate input configuration for running ermod”. Click [Tools]-[Cygwin] in Winmostar to start the Cygwin terminal, where the installation of Gromacs, ERmod, etc. is completed. The “(ERmod directory)” in the procedure is /usr/local/ermod on Cygwin. The etohsolution.top will be the top file saved at the start of the solution calculation. Please use solution_run.xtc and solution_run.log which are stored in the working folder of MD for solution, solvent only, and solute only, respectively.

6.14.14. Import ER

The results processed by Start ER are displayed. After selection, specify the output destination folder specified by Start ER. You can specify units for displaying energy in Unit. Press the Log button to display ERmod’s log file.

6.14.15. Start BAR

Calculate the solvation free energy using the Bennett Acceptance Ratio (BAR) method.

  1. Calculate the solution system (1 solute molecule plus a large number of solvent molecules) using Gromacs. Leave all working folders for each step of equilibration and calculation of equilibrium state.

  2. Select Start BAR.

  3. Specify how to integrate the state (lambda = 1, Full Coupling) in which the solute is not interacting with the solvent (lambda = 0) to the interaction state (lambda = 1, Full Coupling) on the Integration Path tab. Enter the coupling coefficient of van der Waals potential (left) and the coupling coefficient of coulomb potential (right) in the two columns on the left of the Insert button and press Insert to add an integration path.You can delete the integration route by pressing Delete.

  4. In Procedure tab, specify the simulation procedure of each state on the integration path. Specify the procedure of equilibration of solution system (lambda = 1) prepared beforehand in folder unit. Add a folder by dragging and dropping to the Add button or list. Delete folder with Delete button. The calculations performed in the last step of the list are used for free energy calculations.

  5. Press Start to execute MD calculation for each lambda.

  6. After finishing MD calculation of each lambda, to display the result, choose Import BAR.

6.14.16. Import BAR

Display the result of processing with Start BAR. After selecting the menu, specify the destination folder with Start BAR.

The gmx bar is executed in the background and the result is displayed. Please refer to the manual of gmx bar for more detailed behavior.

Unit allows you to specify the unit in which the energy is displayed. If you press Log button, the log file of gmx bar will be displayed. The displayed graph shows the change in free energy between the state in which the solute is not interacting with the solvent (lambda=0) and the state in which it is interacting (lambda=1).