6.11. ¶
menuIt 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.
6.11.1. 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-L, 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.
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 edit the force field information with a text editor and customize it, first save this file using this function, and edit the top file for Gromacs and the data file for LAMMPS with a text editor etc. .
- Next, in case of Gromacs, select Use parameters written in topology file and click OK button. Then you will be asked for the location of the top file, so open the top file you saved and edited earlier.
- In case of LAMMPS, select Use parameters written in file opened on main window and click: guilabel:` Next> button. Then, :guilabel:`Select force field appears. Select the general type of force field to use and click the OK button.
- 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.
6.11.2. 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 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.
- Extending Simulation
Execute a continuous job.
For details, see Run.
- 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 Enabledouble precisionFalse False False False -DFLEXIBLEFalse False False False Extend simulationfrom full-precisiontrajectoryFalse False False False
Minimize NVT NPT NVEdt 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 Enabledouble precisionTrue True True True -DFLEXIBLEFalse False False False Extend simulationfrom full-precisiontrajectoryFalse 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 Enabledouble precisionFalse False False False -DFLEXIBLEFalse False False False Extend simulationfrom full-precisiontrajectoryFalse 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 Enabledouble precisionTrue True True True -DFLEXIBLEFalse False False False Extend simulationfrom full-precisiontrajectoryFalse False False False
Minimize(NMA) NMAdt 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 Enabledouble precisionTrue True emtol0.01 -DFLEXIBLETrue True Extend simulationfrom full-precisiontrajectoryFalse 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 Extending 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
- Make a Backup of Working Directory
- Select when backing up working directory.
- Restore Working Directory
- Click to return working directory to its pre-execution status, such as when a continuous job ends abnormally.
- 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 Extending 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.
6.11.3. Run¶
Run Gromacs. The execution method differs depending on the situation.
- (Default) If Extending 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 Extending 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 Extending Simulation is checked
- The coordinate file (
gmx_mdrun_tmp.gro
) and the topology file (gmx_tmp.top
) in the working directory 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 filewater.out
water.sh
standard output text file. sh filewater.sh
For running Gromacs and its pre/post processingShell script. bat filewater.gro.bat
This is a batch file for executing water.sh
. Working Directorywater_gmx_tmp\
Working directory.The following files are generated in the working directory. 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 iscopied.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 iscopied.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 fileIt is an input file of mdrun.gmx_tmp_mdrun.ndx
Index file for result processing.gmx_tmp_mdrun.edr
Temperature, pressure, energy etc. were storedIt 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 directory **
A working directory 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 directory will be namedaaa_gmx_tmp
.It must be in the same hierarchy as the file opened in the main window.
Processing continues in the working directory 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 directory is
aaa_gmx_tmp
, it isaaa_gmx_tmp1
.- ** Directories without numbers are always up to date. **
The job is run through Winmostar Job Manager.
6.11.4. Open Log File (log)¶
Open the log file (* _ gmx_tmp gmx_tmp_mdrun.log
) of gmx mdrun with a text editor.
6.11.5. Open Stdout File¶
Open the standard output (*. Out
) of the shell script when running Gromacs with a text editor.
6.11.6. 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 window.
6.11.7. 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.
6.11.8. Import Last Coordinate (gro)¶
* _ gmx_tmp \ gmx_tmp_mdrun.gro
.When using this function, the file name of the main window does not change.
6.11.9. 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.
6.11.10. Run Sequential Job¶
Run Gromacs sequentially based on the contents of Configure Sequential Job.
6.11.11. Analyses¶
6.11.11.1. 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 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.
6.11.11.2. 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 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.
6.11.11.3. 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 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.
6.11.11.4. 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 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.
6.11.11.5. 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 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.
6.11.11.6. 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 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.
6.11.11.7. 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 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.
6.11.11.8. 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 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.
6.11.11.9. 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.
6.11.11.10. Chi/DPD parameter¶
Calculate the χ 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.
6.11.11.11. 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.
- Target group
- Calculate the distance, angle, or dihedral angle using the NDX file selected in the Target Group.
- 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 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.
6.11.11.12. 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 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.
6.11.11.13. 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 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.
6.11.11.14. Ramachandoran Plot¶
Select the trr, tpr, and ndx files output by Gromacs to display the Ramachandoran 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 Ramachandoran 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 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.
6.11.12. 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.
6.11.13. Start ER¶
Calculate the solvation free energy using the energy indication (ER) method.
- Execute the calculation of the following three in Gromacs beforehand and leave each working directory. Only use equilibrium state data after finishing equilibration such as energy minimization.
- Solution system (1 solute molecule + many solvent molecules)
- Solvent system (large number of solvent molecules)
- Solute system (one solute molecule)
- Drag and drop the working directory of A. Solution system on the Solution tab. Or, in each column of the xtc, log, top file, press … button to read individual files.
- Likewise select the B. Solvent system file on the Solvent tab.
- 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.
- Select the molecular name of the solute in Solute Name.
- If necessary, specify MPI parallel number at free energy calculation from Options button.
- 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.
- 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 findermod_remote_*
under the folder wherewinmostar.exe
is placed and the result is transferred from the remote server.- After calculating the free energy calculation, to display the result, select the Import ER menu.
6.11.14. Import ER¶
6.11.15. Start BAR¶
Calculate the solvation free energy using the Bennett Acceptance Ratio (BAR) method.
- Calculate the solution system (1 solute molecule plus a large number of solvent molecules) using Gromacs. Leave all working directories for each step of equilibration and calculation of equilibrium state.
- Select Start BAR.
- Specify how to integrate the state (λ = 1, Full Coupling) in which the solute is not interacting with the solvent (λ = 0) to the interaction state (λ = 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.
- In Procedure tab, specify the simulation procedure of each state on the integration path. Specify the procedure of equilibration of solution system (λ = 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.
- Press Start to execute MD calculation for each λ.
- After finishing MD calculation of each λ, to display the result, choose Import BAR.
6.11.16. 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 (λ=0) and the state in which it is interacting (λ=1).