[gmx-users] peptide ligand

Justin Lemkul jalemkul at vt.edu
Sat Oct 7 18:33:33 CEST 2017

On 10/5/17 3:52 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> I performed NVT equilibration for 300 ps , it was done successfully. Yesterday I wanna do NPT equilibration , so used your npt.mdp file in the GROMACS tutorial and replaced energgroups and tc-groups by Protein and Protein water-ions, respectively, specified nstep = 150000 , but when I entered, noticed I had md.log file not npt.log. and it runs to 272000 steps . Why?Would you please help me how come it runs this way?

In the absence of your exact sequence of commands, there's nothing to 
say other than you've probably lost track of what you (think you) are doing.


>        From: Justin Lemkul <jalemkul at vt.edu>
>   To: gmx-users at gromacs.org
>   Sent: Wednesday, 4 October 2017, 15:19:38
>   Subject: Re: [gmx-users] peptide ligand
> On 10/3/17 1:51 PM, farial tavakoli wrote:
>>    blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Because in tuturial , energygroups = protein JZ4So I think ,I have to seperate my ligand and Protein in .mdp files and determine H bonds?
> It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds,
> then you can create an .ndx file later for use with gmx hbond.
> -Justin


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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