[gmx-users] DPOSRES not working
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..
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
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"
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users