[gmx-users] POPC number

Jochen Hub jhub at gwdg.de
Tue Sep 16 17:40:30 CEST 2008

chris.neale at utoronto.ca wrote:
>> 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.
> A hexagonal box? Great. How does one go about constructing that? Is this
> a cylinder-like box with hexagonal shape or just a triclinic one? In the
> triclinic case, does the PBC membrane turn out as it should?

Hey Chris,

a hexagonal box is a special case of a triclinic one: Here we go:

echo "CRYST1  90.0  90.0   40.00  90.00  90.00  60.0 P 1           1" >
genbox -cp x.pdb -cs tip4p -o filled.pdb
echo 0|trjconv -f filled.pdb -o compact.pdb -ur compact -s filled.pdb
pymol compact.pdb

Have fun,

> Thanks,
> Chris.
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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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