[gmx-users] Calculating Distance

Justin Lemkul jalemkul at vt.edu
Mon May 16 13:52:02 CEST 2016

On 5/16/16 3:20 AM, Sanket Ghawali wrote:
> Dear, gmx-users,
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
> Any suggestions on how to go about doing this?

Calculating distances is what the gmx distance program is for.  Simply obtain 
the COM distance between the micelle and peptide (or any subset of atoms that 
makes sense).



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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