[gmx-users] large VCM(group rest)

[Jochen Hub]

Carla Jamous wrote:
> Hi,
> when I get the error message: "water molecule cannot be settled",does 
> it have to do with the SETTLE parameter in gromacs?
> If yes, does anyone know how to fix this?
No, that probably means that you have clashes (atomic overlaps) in your 
system which cause huge forces. Track down which atoms cause the error 
message and remove the clashes.

If that error message appeares during energy minimization, using 
flexible water may help. Define -DFLEXIBLE in the mdp file, and check in 
the spc/itp4p/tip3p.itp file if flexible water molecules are actually 
defined.

Good luck,
Jochen



>
> Carla
>
> On Thu, Oct 1, 2009 at 4:46 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Carla Jamous wrote:
>
>         Hi,
>         I have a problem, I'm running EM, it works but when it comes
>         to doing position-restrained MD, it gives me this error message:
>
>         Segmentation fault
>         Large VCM(group System): -1293135642624.00000,
>         358859374592.00000, -846768177152.00000, T-cm:  6.13428e+26
>
>         I searched the archives, it says to check-out:
>         oldwiki.gromacs.org <http://oldwiki.gromacs.org>
>         <http://oldwiki.gromacs.org>
>
>         but this site doesn't exist anymore.
>
>
>     All of the content has been moved to the new site, albeit a very
>     different organization system.  You should still be able to find
>     it with a bit of digging.
>
>
>         So please can anyone give me the answer to this problem?
>
>
>     The problem is that your system is suddenly moving very fast,
>     probably blowing up.  Without a further description of the system
>     and seeing your .mdp file, it's hard to say what the root problem is.
>
>     -Justin
>
>
>         Cheers,
>         Carla
>
>
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>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
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-- 
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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