Problem while using MARTINI force field with NAMD 2.8

From: rohan uttarwar (rohan.uttarwar_at_wayne.edu)
Date: Tue Jul 12 2011 - 11:42:14 CDT

Hi NAMD Users,

I am trying to replicate the simulation and results of coarse grained
hexadecane molecules with standard MARTINI force field parameters that are
published by Marrink (ref. http://pubs.acs.org/doi/abs/10.1021/jp036508g). I
am able to run the simulation only till the timestep of 8fs. For the
timestep bigger than 8fs I get the error "Periodic cell has become too small
for original Patch grid". But the published results are obtained by running
the simulation at 40fs. Although I found out that if I increase my
Nose-Hoover Langevin piston pressure controls of LangevinPistonPeriod to 500
and LangevinPistonDecay to 250, my simulation runs well upto 40fs. But, it
reduces the fluctuation of my simulation box and I dont get the right
density of the system.

I have attached my NPT simulation configuration file and parameter file with
MARTINI forcefield.

Could anyone help me with why I have to increase my barostat settings to run
the coarse grained simulation at higher timestep? Any kind of suggestion or
advice would be greatly appreciated.

Regards,
Rohan.

-- 
Rohan G. Uttarwar
PhD Student
Dept. of Chemical Engg & Material Science,
Wayne State University,
Detroit, MI.


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