[gmx-users] large VCM(group rest)

[Justin A. Lemkul]

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?
> 

It means the SETTLE algorithm is failing for some particular water molecule. 
Something in your system is blowing up, i.e. it is unstable and causing 
seriously bad collisions across your box.  See here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

As I said before, if you want more detailed advice, describe your system and 
post the .mdp file you're using.  Sometimes these errors occur because 
parameters are set incorrectly.

-Justin

> 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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> 

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

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

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