[gmx-users] energy minimization

Jamie Seyed jamie.seyed at gmail.com
Wed Aug 12 15:27:05 CEST 2009

Dear all, Thanks for all comments. I will check again all steps for my
previous simulation with right files (according to Mark) and then I will let
you know if I got the same problem (I am not working on proteins).
Another question:
--After energy minimization step for in-vacuo run, Should I do still
position restrained MD, since I want the bond length be fixed
--After pr-md in mdrun step for in-vacuo simulation, is it true that I will
get the movement of my molecule in vacuum?? I appreciate your help/Jamie

On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi,
> On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham<Mark.Abraham at anu.edu.au>
> wrote:
> > Jamie Seyed wrote:
> >>
> >> Dear all,
> >> I performed an md simulation but it crashed at the beginning because
> >> according to it "system was exploding". Also when I tried to see the
> >> system
> >> by ngmx, there was no water anymore and it was only the molecule sitting
> >> in
> >> the box(after grompp and before mdrun it was a box of water plus the
> >> molecule)!!??
> >
> > So you used a wrong file at some point... name your files carefully, and
> use
> > them carefully.
> Maybe xtc-grps was set to "protein"? That wouldn't be related to the
> problem. But did the crash occur directly, at step -1/0/1, or did the
> system run at least for a few steps? What exactly were you doing?
> Please copy-paste your command lines, your .mdp file and the mdrun
> output (not the log file yet, please).
> Cheers,
> Tsjerk
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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