On 9/7/17 8:45 AM, Sergio Manzetti wrote:
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..
confout.gro is the final frame, re-wrapped for PBC. So it may "look"
different from the final frame of the trajectory, but it's not.
Unless you actually provide answers to the questions I asked and any
actual commands you're issuing (e.g. what did you do when you say
"produced by gmx trjconv" for instance?), then there's nothing anyone
here can do to help you. We can't see what you're seeing or interpret
what's in your mind :)
-Justin
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
6894 Vangsnes
Norge
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" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
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-requ...@gromacs.org.
