Problem while using MARTINI force field with NAMD 2.8

From: rohan uttarwar (
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. 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.


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

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