6.13. MD ‣ Amber menu

It is a menu related to Amber.

Since Winmostar runs Amber on the Cygwin environment, in order to use this function, you need to set up CygwinWM is required.

6.13.1. Configure LEaP

Use tLEaP to set conditions for creating coordinate (crd) and topology (prmtop) files. Select each item, specify it, and click the [OK] button.

Force Field
Select the type of force field.
Add Na +
Specify whether to add Na ion, and specify the number.
Add Cl-
Specify whether to add Cl ions and specify the number.
Solvate
Specify whether to add water molecules.
Box/Octahedron
Specify the box type.
Solvent
Specify the type of solvent.
Distance
Specify the distance between the solute and the box boundary.
Other LEaP Commands
Write other LEaP commands.

6.13.2. Run LEaP

Create coordinates (crd) file and topology (prmtop) file using tLEaP. (Crd file name except extension) Create a working folder named _leap_tmp, and processing will be done in that folder.

6.13.3. Configure sander

Set conditions for executing calculation by sander. Select each item, specify it, and click the [OK] button.

Basic
imin
Specify whether to perform energy minimization.
igb
Specify the solvent model.
ntb
Specify whether it is a periodic boundary condition or not.
ntt
Specify temperature scaling.
times
Specify the initial temperature.
temp0
Specify the reference temperature.
I NSTL
Specify the number of MD steps.
Advanced
maxcyc
Specify the maximum number of cycles.
NCYC
Specify the number of cycles using the maximum gradient algorithm.
gamma_ln
Specify the collision frequency γ.
DT
Specify a time step.
cut
Specify the cutoff distance.
ntpr
Specify output frequency such as energy value, temperature.
ntwx
Specify how often the coordinates are output to the trajectory file.
QM/MM
Use qmmm
Set ifqnt = 1, add &qmmm namelist, and enable the setting for QM/MM/MD calculation.
qm_theory
Select the calculation method used in the QM region.
qmcharge
Specify the net charge of the QM area.
qmshake
Specify the application of the SHAKE method to the H atom in the QM region.
qm_ewald
Specify the application of the Ewald method to the QM region.
qm_pme
Specify the application of the PME method to the QM region.
qmmask
When you press the [Set] button, the atom selected on the main window is set as the QM area. Blue atoms selected by Ctrl + drag on the main window are targeted.
Misc
Other Settings
Write the other settings.

6.13.4. Run sander

Run sander. (Crd filename excluding extension) Create a working folder named _amb_tmp, and processing will be done in that folder.

The job is run through Winmostar Job Manager.

6.13.5. Animation

Import the coordinates of the trajectory from the PDB file converted from mdcrd file with ptraj.

For the animation display operation method, see Animation window.

6.13.6. Energy Plot

Display the energy graph from the calculated log file.

Please see Energy Plot window for how to operate subwindow.

6.13.7. Import Coordinate File

Load Amber coordinates (crd) file and topology (prmtop) file and display them in the main window.