[gmx-users] How to make a membrane system with 512 DPPCs
Peter C. Lai
pcl at uab.edu
Wed May 25 15:18:27 CEST 2011
On 2011-05-25 07:58:18AM -0500, 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?
> 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.
I don't do anything with DPPC (yet), but another thing that might be doable
is take the POPC template from VMD's membrane plugin and substitute the
oleoyl chain with a copy of the palmitoyl chain, then use the membrane
plugin to create the bilayer (it takes Angstrom dimensions for the bilayer
size), strip the waters, parameterize the single dppc to an itp, genbox
the # of waters you care for, then equilibrate...
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | BEC 257
Genetics, Div. of Research | 1150 10th Avenue South
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
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