[gmx-users] energy minimization

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 12 09:53:07 CEST 2009


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).



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

More information about the gromacs.org_gmx-users mailing list