From: Karteek Bejagam (karteek4_at_vt.edu)
Date: Tue Apr 11 2017 - 13:26:05 CDT
Hi,
set popc [ atomselect top { resname POPC} ]
set all [ atomselect top all]
set move [ vecscale -1 [ measure center $popc]
$all moveby $move
pbc wrap -all -compound res -center origin
Best,
Karteek
On Tue, Apr 11, 2017 at 2:08 PM, Mihaela Drenscko <quo.physics_at_gmail.com>
wrote:
> Hi,
>
> 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,
> Mihaela
>
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