Re: lipid centering

From: Vermaas, Joshua (
Date: Tue Apr 11 2017 - 13:23:05 CDT

Hi Mihaela,

If you have a bilayer, I'd pick 1 POPC residue, center it around that, and then center it around the whole bilayer.
pbc wrap -center com -centersel "resname POPC and residue 1" -all ; #You'll need to pick a residue.
pbc wrap -center com -centersel "resname POPC" -all


On 04/11/2017 12:17 PM, Mihaela Drenscko wrote:

At the beginning of simulation I had solvated POPC, with POPC between two water layers. Occasionally I've got water in the center and POPC above and below water. I tried to center POPC using:

pbc wrap -center com -centersel "resname POPC" -all
pbc join fragment -all
pbc join fragment -bondlist -all

Positioning of POPC and water remain unchanged. What do you suggest I do for centering?

Thank you very much,

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