[gmx-users] peptide ligand

farial tavakoli farial.tavakoli at ymail.com
Wed Nov 8 18:58:10 CET 2017

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear justin
I am tryinig to analyz minimum distance between periodic images, so need a new .xtc file which has not jumps. I isseued this command:Gmx trjconv -s .tpr -f .xtc -o new.xtc -center -pbc molI didnt need to create an index file, because my protein and peptide ligand are merged. But when I bring the .gro  and new.xtc files  to vmd, the new.xtc file has just a frameWould you please help me how come this xtc file has just a frame and what kind of command I have to issue to generate a new one? 
Thanks in advanceFarial

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On Saturday, October 7, 2017, 8:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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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