[gmx-users] protein XYZ dimension function of time

[Justin Lemkul]

On 1/11/17 3:16 AM, atanu das wrote:
> Hi All,
> Is there a simple way to calculate a protein's X, Y, and Z dimensions from a trajectory as a function of time (not the box vector, the protein dimensions as in how the protein spreads itself in the 3 directions as the simulation progresses i.e. XX, YY, ZZ)? I see that GROMACS has an option to estimate protein volume as a function of time, but I need to know how the individual dimensions change as a function of time.

gmx traj extracts coordinates, from which you can find maximum and minimum 
values along any axis.  The output is a bit unwieldy but easily parsed.

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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