[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

J B john.b.86 at hotmail.com
Tue May 8 15:48:04 CEST 2012

I assume that you mean pull_pbcatom0...
Nothing changes when I set this to an atom index I am afraid.
I saw that you had use pull_geometry=cylinder in your recent JACS paper.
Would it be too much to ask to see those pull settings?
I simply cannot get the molecule to stay at the desired z-position...

> Hi,
> we had similar trouble some time ago, and we could solve it by using a 
> good PBC atom. Make sure that your pbc_atom is in the very center of 
> your membrane.
> Btw, using "distance" to compare with "cylinder" is a bad test, since it 
> does something very different (the distance is the same at z=com-1 and 
> z=com+1. I would use "direction" or "position" for your test. You can 
> also use position/direction for the umbrella simulations, you'll 
> probably get similar results to the geometry "cylinder", but you'll also 
> have to make sure your pbc_atom is fine.
> Cheers,
> Jochen
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