coarse-grained MD

From: Demet Akten (demet.akten_at_gmail.com)
Date: Fri Feb 11 2011 - 03:34:56 CST

Dear All,

We are currently running a residue-based CG simulation of a membrane
protein system with explicit solvent and 10 fs timestep. We are using
Langevin Piston for Temperature and Presssure control. When the
program becomes unstable, we restart the simulation from the last
written snapshot using all the files .vel, .coor and .xsc. We check
that the final written energy values of the previous run match the
initial values of the next run. Surprisingly, the new run goes on
without any further problem. Should we worry about the fact this new
run is not the continuation of the previous run, but a completely
independent run? Is there any randomness in Langevin Piston dynamics?

Thanks a lot!

Demet

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