[gmx-users] Selecting box dimension and COM position - Pull Code

Justin Lemkul jalemkul at vt.edu
Mon Oct 27 01:19:36 CET 2014

On 10/26/14 3:43 PM, Agnivo Gosai wrote:
> Dear Users
> I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am
> using the methodology described therein for running my own simulations.
> It is explained that :-
> "GROMACS calculates distances while simultaneously taking periodicity into
> account. This, if you have a 10-nm box, and you pull over a distance
> greater than 5.0 nm, the periodic distance becomes the reference distance
> for the pulling, and this distance is actually less than 5.0 nm! This fact
> will significantly affect results, since the distance you *think* you are
> pulling is not what is *actually* calculated."
> Are there any guidelines for assigning the COM position of my biomolecule
> complex and the x,y,z dimensions of my simulation box keeping in mind the
> above explanation.
> Or I should go about it in a trial and error basis?

Trial and error is an awfully expensive way to determine what you need to do, 
when it's rather straightforward to figure out.  Determine the length of the 
reaction coordinate you need.  Based on the length of that vector in the 
dimensions along which the pulling takes place, it is simple to figure out the 
minimum size of the box in each dimension.  If using pressure coupling, add a 
small buffer to the size to account for fluctuations.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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