[gmx-users] Problem in equilibration for membrane system

[Mark Abraham]

Bing Bing wrote:
> Dear All,
> I'm running the protein complex with POPC system. NVT (100ps) and NPT 
> (200ps) were done with restraint on the protein follow by 1000 ps of NPT 
> without restraint on protein. The trajectory was checked in term of 
> pressure, potential, area per lipid ....were checked and everything 
> seems ok (potential almost plateu, area per lipid close to experimental 
> value). I proceeded with md (similar to Justin's tutorial) for 1 ns. The 
> simulation stop around 800ps with the range checking error.

OK so look at the collective variables, and/or trajectory to find 
evidence of the problem. The most likely explanation is that your 
protein was unhappy in the restraints, of course. Perhaps you should try 
some vacuum EM before you embed it in the lipid, or some such.

> I'm using 
> gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired to be more gentle 
> while releasing the restraint.Different stepwise of releasing the 
> restraint during NPT were tried and followed by production MD, all the 
> simulation stop or i shall said it crashed around ~800ps with the same 
> error (range checking error). I'm out of idea what is the problem here. 
> Please advice.

Range checking is just one of many things that can be the first thing to 
break when there's an underlying systemic problem.

Also, unless you need scientific continuity, 3.3.2 is about 4 years 
old... 4.0.5 will be much faster!

Mark