[gmx-users] peptide ligand

[‪farial tavakoli‬ ‪]

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?


      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

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

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