[gmx-users] pbc visualization advice

Peter C. Lai pcl at uab.edu
Fri Jan 6 09:51:30 CET 2012

Hi all:

I'm running a diffusion simulation involving a membrane protein and may be 
having a problem with the trjconv workflow.

I have some molecules I'd like to study the diffusion of across the membrane
(if it happens) and/or see if they interact with the membrane protein inside
the membrane.

So I trjconv -pbc whole, then trjconv -pbc nojump. After this, the trajectory
is continuous but of course the water and some of the ligands are leaving
the box.

What's the next step I should perform to make a good visualization so that
the box looks intact and the protein remains centered? If I try to use
something like -pbc mol -center it forms a nice box but now I have molecules
that diffuse into the mirror and makes it look like they have diffused
into the intracellular space (bottom of the mirror) which does not look good.

Will clustering help me? 

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

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