residue based coarse-grained simulation

From: Demet Akten (
Date: Tue Nov 09 2010 - 07:03:05 CST

Dear All,

We try to simulate a residue based coarse-grained simulation of a
protein+lipid+water+ions at constant NPT. We tried different protocols
for simulation, such as putting constraints on protein, increasing
time steps, increasing the periodic box, etc. Unfortunately, we cannot
prevent some atoms from moving too fast. Can you give us any
suggestion on how to proceed with the simulation protocol?



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