[gmx-users] How to calculate the COM and box vectors in umbrella sampling

Justin Lemkul jalemkul at vt.edu
Thu Jul 10 14:32:48 CEST 2014

On 7/10/14, 1:47 AM, Maziya Ibrahim wrote:
> Dear all,
> I want to carry out umbrella sampling on a protein-ligand complex, that was
> already subjected to regular MD simulation for a few nanoseconds.
> How should I calculate the optimum pull distance and box size to be used?

The length of the vector should be sufficient to at least preclude short-range 
nonbonded interactions and any water-mediated effects between the protein and 
ligand.  It's not possible to achieve total non-interaction in a periodic cell 
with PME.

> Is there a default value that can be applied?


> Also how to calculate the center of mass of the protein and the box vectors?

g_traj -ox -com with suitable index groups will tell you the COM positions of 
anything, though simply using the protein as the reference group may not be 
appropriate, depending on the geometry of the system.  The box vectors are in 
the coordinate file, either the final line of a .gro file or the CRYST1 line of 
a .pdb file.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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