Winmostar tutorial
Gromacs
Viscosity・Dielectric constant
V8.007
X-Ability Co., Ltd.
question@[Link]
January 15, 2018
Summary
In this tutorial, we will calculate viscosity and dielectric constant of liquid of water. Product run
will be executed on a NVE ensemble (no restraints on temperature/pressure) to calculate
physical properties sensitive to delicate movements of molecules. We will also show
equilibration procedure for calculating NVE ensemble under target temperature/pressure.
①-D
①-C
①-A ①-B Equilibration
Equilibration
Equilibration Equilibration constant Density adjustments
constant
energy minimization constant temp. MD temp./pressure MD
temp./pressure MD
(obtain avg. vol.)
①-F ②
①-E
Equilibration Product run
Equilibration Temperature
No temp./pressure No temp./pressure Analysis
constant temp. MD adjustments
restraints restraints
(speed regeneration)
(obtain avg. temp.)
Notes:
• The number of steps required for equilibration depends on the type of molecule and initial
density varies and may be different from this example.
• To obtain accurate and reproducible results, the calculation requires long simulation times.
• The method for interaction calculations and/or the force field also affect the simulation results.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
Configuration
You must set up Cygwin to use Gromacs on Winmostar.
• Obtain the installer for Cygwin, which contains the all programs needed by
Winmostar, at [Link]
• When you change the installation path for Cygwin from the default one,
specify it on the preference panel.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
I. Build a simulation cell
1. Click MD | Solvate/Build Cell.
2. Uncheck Put the molecule on main window as solute.
3. Click Add Water.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
I. Build a simulation cell
1. Set Enter # of molecules to 500, then click OK.
2. Set Set Density to 0.9, then click Build.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
II. Equilibration (A - C)
1. Select MD | Gromacs | Sequential Job Setup.
2. Set Use preset to Minimize (fast) and click >>> Add >>>
3. Set Use preset to NVT (fast) and click >>> Add >>>
4. Set Use preset to NPT (fast) and click >>> Add >>>
5. After sequentially setting Use presets, click Set.
6. Next, select MD | Gromacs | Start Sequential Job and save files to begin job.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
II. Equilibration (D) + Density Adjustment
1. After the calculation, click MD | Gromacs | Keywords Setup.
2. In the Basic tab, set nsteps to 25000.
3. In the Automatic tab, check box for Rescale box size…
3. Click OK.
4. Click MD | Gromacs | Start Gromacs.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
II. Equilibration (E)
1. After the calculation, Click MD | Gromacs | Keywords Setup.
2. Set Preset to NVT (fast).
3. Click OK.
4. Click MD | Gromacs | Start Gromacs.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
II. Equilibration (F)
1. After the calculation, click MD | Gromacs | Keywords Setup.
2. Set Preset to NVE (fast).
3. In the Automatic tab, check Rescale Velocities to ... .
4. Click OK.
5. Click MD | Gromacs | Start Gromacs.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
III. Product Run
1. After the calculation, click MD | Gromacs | Keywords Setup.
2. On Basic tab, set nsteps to 500000.
3. Click OK.
4. Click MD | Gromacs | Start Gromacs.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
IV. Prediction of Viscosity
1. After the calculation, click MD | Gromacs | Shear Viscosity.
2. Open the default files; repeat 3 times.
3. Click Draw to draw the predicted value of Viscosity.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
V. Prediction of Dielectric Constant
1. After the calculation, click MD | Gromacs | Static Dielectric Constant.
2. Open the default files; repeat 3 times.
3. Click Draw and set Tempareture [K] to 300, then click OK.
The predicted value of dielectric constant will be displayed.
Copyright (C) 2018 X-Ability Co., Ltd. All rights reserved.
