[gmx-users] Helicity over simulation time?

Justin Lemkul jalemkul at vt.edu
Wed Aug 26 11:56:49 CEST 2015

On 8/25/15 10:20 PM, Rajiv wrote:
> Dear all,
> I have performed 200ns simulation for a protein and wants to plot a helicity over simulation time.
> After reading few queries, i have done do_dssp and obtained the scount.xvg which has the all secondary structure as a function time.
> I wonder, how do i only obtain the helicity over function of time as i want to plot the probability distribution of helicity.

You basically have this information - scount.xvg has the number of helical 
residues in each frame.  Divide by the total number of residues and you have the 
fraction of helix over time.



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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