[gmx-users] DPPC bilayer simulation crash

Michael Skaug mjskaug at ucdavis.edu
Thu Apr 5 22:15:03 CEST 2007

I am trying to perform a simulation of 128 dppc in 3655 spc water.
I obtained .pdb and .top files from the Biocomputing website at U.Calgary.
 I do nothing to alter the structure, which must be minimized as it comes
from the end of a 1 ns simulation.  Processing the input files works fine,
but the mdrun always ends somewhere between step 500 and step 3000.  I have
tried adjusting various parameters, such at the time step, tau_p, tau_t and
the compressibility, but nothing has created a consistent run.
I wonder where I should be focusing my time to solve this problem.  Should
I focus on the parameters and structure, or computer hardware/software?

Thanks for any suggestions
--Mike Skaug
University of California Davis

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