[gmx-users] gmx make_ndx - separating pulling groups by fragments

Justin Lemkul jalemkul at vt.edu
Tue Oct 4 14:13:13 CEST 2016



On 10/3/16 11:25 PM, vprytkov wrote:
> Hello! I'm trying to conduct a pulling simulation with two identical proteins
> and centers of mass distance being the reaction coordinate. They are
> distinguished by fragment index in vmd (0 and 1), but the residues in the .gro
> file run from 1 to 178 and again from 1 to 178. How to I used make_ndx command
> to create an index file for the pulling simulation?

Specify their atom numbers.

a 1-x
a (x+1)-y

-Justin

-- 
==================================================

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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