[gmx-users] how to set Restraints

Justin Lemkul jalemkul at vt.edu
Fri Feb 19 14:11:21 CET 2016

On 2/18/16 9:11 PM, Sana Saeed wrote:
> hisir Justin Lemkul  and gmx usersi am stuck in a problem. i am performing MD
> simulation of complex of protein and ligand for binding free energy
> calculation. i have done all the basics of MD, performed all the BEVANLAB
> tutorials for my learning and some other papers examples. but i never dealt
> with binding free energy calculations , so in different tutorials they have
> the complex topology, which is my problem, i made ligand and protein
> topologies but now i dont know how to get distance, dihedral and angle
> restraints, Sir Justin Lemkul you replied me "To include intermolecular
> restraints and bonded terms, just use [intermolecular_interactions] at the
> end of the .top (available in versions 5.1 and newer).  Use global atom
> numbers to define the interactions." can you a little bit explain how to do
> that.Thanks in advance

It's exactly the same as any interaction.  In the .top file:

[ system ]
[ molecules ]
[ intermolecular_interactions ]
[ dihedrals ]
i j k l (parameters) <- here, i-j-k-l are global atom numbers taken from the 
coordinate file



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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