[gmx-users] ERROR ON POSITION RESTRAINED md

[Anton Feenstra]

Raj Badhan wrote:
> Hi
> 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').


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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