[gmx-users] pbc problem

shahab shariati shahab.shariati at gmail.com
Tue Oct 29 17:02:07 CET 2013

Dear Mark

Very thanks for your reply

> To make this clear, center the trajectory on the water and watch the
> time evolution in some visualization program.

I did your suggestion (center the trajectory on the water). Again, drug
molecule is in region (1)in some frames and is in region (4) in other

Dear Justin

Very thanks for your attention

> As has already been stated several times, there is no problem at all.
> The outcome is completely normal, and there are not discrete
> regions (1) and (4).
> It is a continuous block of water via PBC.  The molecule can freely
> diffuse throughout it.

If outcome is completely normal, Can I use this structure for pmf
calculation. I want to calculate potential of mean force, delta G, as a
function of the distance between the centers of mass of drug and the
centers of mass of bilayer.

Best wishes for you.

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