[gmx-users] DPOSRES not working

Sergio Manzetti sergio.manzetti at fjordforsk.no
Thu Sep 7 14:52:56 CEST 2017

It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. 

Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, September 7, 2017 2:28:23 PM 
Subject: Re: [gmx-users] DPOSRES not working 

On 9/7/17 5:28 AM, Sergio Manzetti wrote: 
> Hi Johannes, yes, they are there in both cases: 
> ; Include Position restraint file 
> #ifdef POSRES 
> #include "posre_DNA_chain_E.itp" 
> #endif 

Do you have a position restraint energy term written in your .log file, 
and if so, what is its magnitude? Does your DNA start at the middle of 
the box (GROMACS convention) or at the coordinate origin (like other 
software)? If you watch the trajectory evolve, what happens? Does the 
DNA move a lot or does it just bounce back and forth around its original 
position (suggesting your box is simply too small and any time an atom 
crosses a boundary, you get a jump)? 



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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