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