[gmx-users] pbc problem

[Mark Abraham]

On Oct 24, 2013 8:10 AM, "shahab shariati" <shahab.shariati at gmail.com>
wrote:
>
> Dear jkrieger
>
> I used 2 times trjconv tool:
>
> 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
>
> 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol
-center
>
>
> Dear Mark
>
> I selected all lipid atoms for centering.
>
> With my manner, pbc problem was solved just for lipids and not for drug
> molecule which is put inside water molecules in top leaflet. This pbc
> problem cause to drug molecule be in top and bottom leaflets, while I want
> to study translocation of the drug molecule from water to lipid bilayer.
> I want to solve this problem for drug molecule.

There is only one water region, so "upper" and "lower" don't mean much. If
you just want to see the drug and bilayer in the same PBC cell, then center
on something that is central.

Mark

> If my manner is wrong, please tell me true way.
>
> Best wishes.
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