[gmx-users] pbc problem

[shahab shariati]

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
frames.

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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.