Re: Fwd: conf file for coarse grained simulation

From: Axel Kohlmeyer (
Date: Tue Dec 15 2009 - 02:17:45 CST

On Mon, Dec 14, 2009 at 3:19 AM, Francesco Pietra <> wrote:
> In addition: in agreement with lack of clashes in the system
> protein+bilayer, a minimization at const volume of protein_bilayer
> (where periodicity and PME were suppressed, otherwise the same conf
> input) went to completion, as shown by the final portion of log:


the obvious conclusion of your description is that
you have clashes due to periodicity, i.e. using too
small a simulation cell for your system. please keep
in mind that coase grained "atoms" are much larger
than regular ones and that you thus need a more
"safety" distance when computing the size of a cell.


Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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