Re: residue based coarse-grained simulation

From: Hannes Loeffler (
Date: Tue Nov 09 2010 - 09:37:18 CST

On Tue, 9 Nov 2010 15:03:05 +0200
Demet Akten <> wrote:

> 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?

Well known problem for certain coarse-grained models. Have a careful
look into the literature especially recommendations regarding the use
of (additional) elastic networks.

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