[gmx-users] TP2 problem

farial tavakoli farial.tavakoli at ymail.com
Wed Jan 3 08:06:16 CET 2018

Dear Justin
Thank you for your replying
best Farial

    On Wednesday, January 3, 2018, 4:36:38 AM GMT+3:30, Justin Lemkul <jalemkul at vt.edu> wrote:  

On 1/2/18 4:28 PM, farial tavakoli wrote:
> Dear Justin
> Thank you for replying
> I understood what was the wrong and fixed it. But now I have another problem about CHARMM36 mdp file. I studied http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM for adding new settings to mdp file but I need to understand if It is needed to add these new settings to the mdp file for minimizatin? In fact, I couldnt

The nonbonded settings specified there should be used in all your .mdp 
files when using the CHARMM force field.

> understand what does mean these settings:
> vdw-modifier = force-switchrvdw-switch = 1.0
> Should I add these to the mdp file for minimization?

You should add everything on that page exactly as it appears. If you are 
unclear on what the settings are or mean, read the GROMACS manual and 
CHARMM force field literature.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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