[gmx-users] POPC number

Jochen Hub jhub at gwdg.de
Tue Sep 16 10:58:40 CEST 2008

I guess that depends on the size of your protein. You should have enough
 lipds such that the protein doesn't interact with its preriodic image.
90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
usually had something like 270 POPE molecules, but if you simulate a
smaller protein, less lipids may be sufficient. You may also want to use
a hexagonal box which will allow you have less lipids and water.

cheers, jochen

sudheer babu wrote:
> Hi gmx-users,
> whats the number of POPC molecules should be there after inserting protein
> into popc? In my case 90 popc molecules are there around the protein from
> 128 molecues which I downloaded from Dr.Tielman's website.
> Any suggestion will be appreciated
> Thanks in advance.
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Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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