[gmx-users] pbc problem

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 29 17:54:39 CET 2013

On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
<shahab.shariati at gmail.com>wrote:

> 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.

With pbc = xyz, you do not have two chunks of water. You have one chunk of
water. Where you put the box for visualization is irrelevant to the
simulation. You could align one of the box sides with one of the membrane
surfaces, and now you will see only one chunk of membrane, and one chunk of
water. In that chunk of water the drug goes wherever diffusion takes it,
just like it did inside the membrane.


> ----------------------------------------------------------------------------------
> 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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