Jamie Seyed wrote:
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
(constraints=all-bonds)?
--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
Position restraints are most commonly used to allow solvent to relax around a
structure during initial equilibration. If you're running in vacuo, I don't see
much purpose. It is possible that your molecule will still move; PR does not
mean that you are fixing atoms in place, but instead that you are specifying an
energy penalty for moving the constituent atoms away from their original
coordinates.
-Justin
help/Jamie
On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>> wrote:
Hi,
On Wed, Aug 12, 2009 at 3:06 AM, Mark
Abraham<mark.abra...@anu.edu.au <mailto:mark.abra...@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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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