[gmx-users] How to make a membrane system with 512 DPPCs

Peter C. Lai pcl at uab.edu
Wed May 25 15:32:12 CEST 2011

On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote:
> Du Jiangfeng (BIOCH) wrote:
> > Dear Gromacs Users,
> > There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where?
> If you have a 128-lipid membrane:
> genconf -f 128.gro -o 512.gro -nbox 2 2 1

Wasn't there a warning about PBC and compact structures when using the PDBs 
from Peter Tieleman?

Aren't we supposed to unwrap those structures with trjconv before actually 
using them in any sort of meaningful way? See also
on generating a dummy tpr for feeding into trjconv.

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