[gmx-users] LINCS Warnings in the middle of an MD run
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 13 21:05:27 CET 2001
On Thu, 13 Dec 2001, Christoph Meier wrote:
>One of my GROMACS MD simulations crashed after running stably for almost 4ns (=several
>weeks on our system). The error message I get is this:
>relative constraint deviation after LINCS:
>max 0.000987 (between atoms 3286 and 3289) rms 0.000026
>bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
>I got almost 100 of these LINCS WARNINGs before the system eventually crashed.
>The atoms involved (3286 and 3289) belong to a protonated lysine residue, the topology
>of which was generated in the standard (pdb2gmx) way.
>Does anybody have suggestions as to what I could do to get round this problem ?
>Do you think there is anything wrong with the lysine residue or anything else ?
Have you looked at the pdb files? Anything strange with them? You are not
maybe running redhat linux 6.2 with the standard kernel, are you? In that
case you need to upgrade the kernel.
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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