[gmx-users] what does the error mean
xiaoyi at xray.bmc.uu.se
Wed Nov 5 16:08:00 CET 2003
Thanks for Martina and Anton, after I reduce dt to 0.001ps and add
period bondary condition in my .mdp file, I get the result of long MD
On Thu, 2003-10-30 at 22:13, Martina Bertsch, PhD wrote:
> > xiaoyi li wrote:
> >> Hello,
> >> My system is composed from two proteins, two axt molecules and a box of
> >> water. During the MD run by Gromacs, it is always stopped at 200ps or
> >> less because of error.
> >> At the end of .log file, it shows:
> >> Constraint error in algorithm Lincs at step 10767
> >> t = 21.534 ps: Water molecule starting at atom 45552 can not be settled.
> >> Check for bad contacts and/or reduce the timestep.Wrote pdb files
> >> with previous
> >> and current coordinates
> >> Grid: -2147483648 x -2147483648 x -2147483648 cells
> >> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 211]
> >> What should I do?
> >> Thanks a lot!
> >> xiaoyi
> > Greetings, Xiaoyi.
> > You could try the energy minimization protocol with fully flexible
> > water molecules, i.e., add the following to the .top file:
> > #include flexspc.itp
> > Also, in the .mdp file set:
> > constraints = none.
> > Finally, emstep in .mdp should be small (0.001 per Marcos Villarreal,
> > see an earlier message in the archive).
> > Martina Bertsch, Ph.D.
> > Northwestern University
> > Feinberg School of Medicine
> > Molecular Pharmacology and Biological Chemistry
> > 303 East Chicago Avenue
> > Chicago, IL 60611
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xiaoyi li <xiaoyi at xray.bmc.uu.se>
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