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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