[gmx-users] pbc problem

[Mark Abraham]

As Justin said, there is no actual division between region 1 and 4.
Apparently you got the free diffusion you asked for! :-)

Mark


On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati
<shahab.shariati at gmail.com>wrote:

> Dear Mark
>
> Thank for your reply.
>
> If I show my system as 4 regions, my system before equilibration is as
> fallows:
>
> region (1): water + drug
> region (2): top leaflet of bilayer
> region (3): bottom leaflet of bilayer
> region (4): water
>
> After equilibration, drug molecule exits region (1) and enters region (4).
>
> Please tell me how to fix it? Which options of trjconv are appropriate
> for this problem?
>
> Best wishes
> --
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