[gmx-users] gmx 3.1 vs 3.0 for new DPPS model

David L. Bostick dbostick at physics.unc.edu
Thu Apr 4 17:14:35 CEST 2002

Hello all,

I am working on a model of DPPS lipid for bilayers and testing them against
some developed with AMBER OPLS parameters for consistency.  .. IN any
case, To start, I am constructing a DPPS bilayer with Na+ ions.  The system
is neutral.

I have been trying for many days to build the bilayer with gmx3.1 and those
of you who build bilayers know that it's tough to get all of the "hot
spots" out of the system and to get the tails to melt appropriately.
During the construction in gmx3.1, I have been using a timestep of .0001 ps
and doing runs in the NVT ensemble.  The system will be at a reasonable
temperature for a while and then at the next step (literally, I watch step
by step) the temperature will become something like 10^11 and the program
will cut out usually with some warning about the velocity of the center of
mass being too high.

In a desperate attempt to simply try something different, I recompiled
gmx3.0 and have been able to successfully construct the bilayer throughout
using a 0.001 ps timestep.  I have just now moved it to 0.002 ps and it's
just fine.  I have no idea what could have changed between the two versions
that could cause such a difference.  Can someone help?


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

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