[gmx-users] LINCS Warnings in the middle of an MD run

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 13 21:36:33 CET 2001

On Thu, 13 Dec 2001, Christoph Meier wrote:

>You wrote:
>> Have you looked at the pdb files? Anything strange with them? 
>The residue+its surroundings look normal before I get
>the errors. In the pdb files that were produced
>when ths run crashed, two hydrogens in the lysine are very close to each other.
>I can't see any other irregularities.
Is there any strong interaction of the lysine side chain with something?

>You wrote:
>> You are not maybe running  with redhat linux 6.2
>> the standard kernel, are you?
>I don't think so.
>How would this affect the stability of my the MD run ?
There are bugs in that kernel that cause ureliable floating point
calculations. It could also be a hardware problem, but of course I can not
totally exclude a problem in the gromacs software.

One workaround may be to run tpbconv on your trr and tpr to make a
continuation run. If you use t coupling the runs are not 100% identical,
so it may or may not continue past the point where it stopped. If it
crashes again you can run the same tpr on another computer to see if it is
reproducable. If it is reproducible (and not after a few weeks) you may
forward me the tpr...

>Thanks very much for your help !
>Best wishes,
>gmx-users mailing list
>gmx-users at gromacs.org
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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