RE: POPC bilayer- System size

From: JC Gumbart (
Date: Sun Jun 03 2007 - 18:35:19 CDT

What do you mean by separated? A snapshot of the system may help.

If you are using the minmax of the lipids (or "all") to set the dimensions,
it will be too big. If that is the problem, try using the minmax of water
to set the x and y dimensions.

-----Original Message-----
From: [] On Behalf
Of Purushottam Dixit
Sent: Sunday, June 03, 2007 5:46 PM
Subject: namd-l: POPC bilayer- System size


I want to simulate a POPC bilayer (size 130X130 Angstrom) using
periodic boundary conditions. If I use the VMD pluggin to generate the
membrane of the required size, due to the randomness and slight
distortions of the layer, the dimensions are not exactly 130X130.

If I try to to run a simulation using approximate dimensions
(estimated by the minmax function) under periodic boundary conditions,
the bilayer gets seperated because of the apparent anisotropy of the
repeat motif. It is very important for me not to use a large bilayer
and forget about periodicity. Any suggestions?


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