[gmx-users] Problem in equilibration for membrane system

Bing Bing jarbing09 at gmail.com
Wed Oct 7 09:33:59 CEST 2009

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. 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.

thanks in advance.

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