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 <[email protected]
<mailto:[email protected]>> 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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---------------------------------------------------
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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