[gmx-users] ERROR ON POSITION RESTRAINED md
feenstra at chem.vu.nl
Wed Sep 17 10:24:03 CEST 2003
Raj Badhan wrote:
> I've setup my protein within a water box and am running the
> position restrained md simulation using mdrun and pr.mdp.
> I get the following error message:
> step 0, time 0 (ps) LINCS WARNING relative constraint deviation
> after LINCS: ...followed by a list of amino acids which have rotated
> by over 30 degrees.
> followed by a step 1, time 0.002....and then the simulation crashes.
> I'm doing this with a dimer of a protein I am interested in.
> I'm not sure what is going on, apart from the obvious, and any
> suggestions would be appreciated.
Could you successfully minimize your system?
My standard equilibration procedure for protein MD is:
1) EM protein in vacuum,
2) add water (genbox),
3) EM protein + water,
4) MD+PR prot+wat,
Optionally, I add PR also in the EM steps, and do an additional non-PR
EM before MD+PR (step '3b').
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