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

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 15:00:32 CEST 2011

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


> We also tried to build a 512 lipids system manually.
> First by means of VMD where we combined 4 128 pre-assembled membranes together thus creating one single file with 512 lipids, however during energy minimization the whole membrane shattered and scattered bits of lipid outside the defined box dimensions. Another problem was that after ionization 2 of the membranes parts (128+128 lipids) were merged and 1 got deleted.
> The second method was by running a self-assembly simulation (270 ns) on gromacs using the Martini forcefield, yet we did not get a single membrane but double bi-layers with water in between. 
> Any suggestion is appreciated.
> Albert and Jiang.-- 
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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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