Re: Fwd: conf file for coarse grained simulation

From: Francesco Pietra (
Date: Tue Dec 15 2009 - 02:40:55 CST

Hello Axel:
Indeed I took that into account when devising the procedure, although
a Boundary of 24 and Box Padding of 15 (12 in a repeated simulation)
seemed to me to give a gap enough between cells. The analysis was:

molinfo top set a 103
molinfo top set b 123
molinfo top set c 93

Graphic Representations ... Periodic... select all x,y,z

Also, I was terrified by the number of water beads already present in
the above configuration.

In answer to Peter also the full set of parameters used for solvation:
Segment ID Prefix WT
Boundary 24
Box size: Use molecule dimensions
Box padding: 12 throughout
Use non standard solvent:
Solvent box pdb: cgwat.pdb
Solvent box psf: cgwat.psf
Topology: (added of "Nxg Nxx Nxg 2.988 92 in the Angle sectio)
Side length: 40 (I did not check this with VMD; with Chimera, more or
less, it corresponds)
Key selection: name H2O


On Tue, Dec 15, 2009 at 9:17 AM, Axel Kohlmeyer <> wrote:
> 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:
> francesco,
> 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.
> cheers,
>    axel.
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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