[gmx-users] Problem with membrane simulation
nerafiee at ipm.ir
Tue Feb 7 16:41:43 CET 2017
I have a major problem with building my system which contains two parallel bilayers. If I use different servers such as CHARMM-GUI or ATB or any other, I will have gro and top file and I can concatenate two bilayers into one simulation box. But when I fill the box with water (using $gmx editconf ... and $gmx solvate ...), I will have water all over the box, and it is not desirable. I want to have water moleculed just above and under bilayers. On the other hand, if I use Packmol software, I will get my desirable coordinate file, but I cannot produce .top and .gro with pdb2gmx according to what Lindahl suggest in this video: https://www.youtube.com/watch?v=nwMiqP4g1Zo
Has anyone worked with Packmol for lipid bilayers?
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