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 <[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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--
========================================
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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