[gmx-users] segmentation fault with lincs warning
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 14 13:10:37 CEST 2008
ANINDITA GAYEN wrote:
> Dear all,
> I have an dmpc bilayer equilibrated for 12 ns. I have built a CHAPS molecule in the OPLSAA force field and inserted it in the equilibrated bilayer. There was no problem till the minimisation, but when i started the MD, the job escaped out with a lincs error
> Initializing LINear Constraint Solver
> number of constraints is 6572
> average number of constraints coupled to one constraint is 3.3
> Rel. Constraint Deviation: Max between atoms RMS
> Before LINCS 0.817519 4126 4128 0.017115
> After LINCS 30.145958 17066 17068 1.789056
> Step -2, time -0.004 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> max 30.145958 (between atoms 17066 and 17068) rms 1.789056
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 4128 4129 31.1 0.1571 0.1600 0.1530
> 16859 16858 36.1 0.1529 0.1022 0.1529
> 16858 16859 36.1 0.1529 0.1022 0.1529
> 16897 16858 49.2 0.1523 0.1495 0.1529
> [all the atoms and bonds in the error list are for CHAPS]
> Do i have the problem in the topology file? I have inserted 4 chaps mole cules without replacing the dmpc molecules, i.e. 4 chaps with 128 dmpc molecules in the bilayer. Is this causing any steric problem?
This is a *very* common problem, and a lot of potential solutions are in the
list archive and wiki site. As such, I won't list them here, but you can
certainly find them within a few minutes (or seconds) of searching.
If you have a pre-equilibrated bilayer, and inserted molecules into it without
removing any lipids, you probably have very severe atomic overlap. But as I
said, search the archive and try the things you find there.
> Please suggest a way to get out of the problem. If you want, i can upload my topology and mdp files in the next mail.
> Yours truly,
> anindita gayen
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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