[gmx-users] box size for simulation of membrane protein

Alan Dodd anoddlad at yahoo.com
Fri Jan 12 12:42:02 CET 2007

---- Original Message ----
From: Mohamed Osman <osmangmx at gmail.com>
To: gmx-users at gromacs.org
Sent: Thursday, January 11, 2007 10:49:29 PM
Subject: [gmx-users] box size for simulation of membrane protein

My questions: 
1. Protein is closer to one edge than the other.  Does this make any difference?  
   The solvants are part of equilibritaed lipid.

-Shouldn't do.  It's still the same distance from its periodic image on each side, which is what matters.  As long as it's in the correct place in the bilayer, I don't believe there are any 'edge effects' in the implementation of PBC in gromacs you need to worry about.

Along protein axis:
   a.  The periodic image is 1.43 nm away.   (along protein axis) 
   b.  The distance between the protein and its mirror image is:     0.8 nm  on one side and 2.0 nm on the other side?   (These affect PME - coulmb interactions).  Will these cause trouble?

-The minimum protein-image distance is all that matters.  It doesn't matter how close the protein is to one side of the box - if it's closer on one side, it's further on the other.  Unless you mean different distances on the x and y axis?
-As far as I know, PME sums out to infinity, so you can't really change that.  BUT:

2. Is it necessary to keep the protein at least 1.5 nm away from the edges normal to z-axis?  This more than doubles the number of solvant molecules.    ---- 

I have simulations with less than 50,000 atoms (protein, solvants, and KcsA).  But no one realy says much about the box sizes.   

What is the common practice?  Please give examples?
How much compromise is acceptable ?  
-The official requirement is for the minimim distance from protein to its periodic image to be double the cutoff, so that no atom feels forces from more than one image of the protein.  However, you can probably get away with reducing that minimum distance to slightly more than the cutoff (1.5nm in your case) which just stops the protein from interacting with its own periodic images.  Most people work on this basis, on the grounds it probably doesn't matter if the water molecules are 'feeling' more than one protein.  It's a judgement call really, depending on how badly you want it to run faster vs how much you lose by making it do that.

"It is common to compormize in this respect  !!!"

Mohamed Osman 

Professor of Electrical Engineering
Washington State University
Pullman, WA 99164-2752

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