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
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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