[gmx-users] energy minimization

[Justin A. Lemkul]

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 <tsjerkw at gmail.com 
> <mailto:tsjerkw at gmail.com>> wrote:
> 
>     Hi,
> 
>     On Wed, Aug 12, 2009 at 3:06 AM, Mark
>     Abraham<Mark.Abraham at anu.edu.au <mailto: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
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================