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

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 15:36:13 CEST 2011

Peter C. Lai wrote:
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> on generating a dummy tpr for feeding into trjconv.

Sure, you need an intact starting structure before doing anything like this. 
There are other sources of membranes, not just Tieleman's site, many of which 
have already been corrected for PBC effects.  The OP did not state the source of 
the 128-lipid membranes in question, so I did not presuppose any particular 
starting configuration.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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