[gmx-users] position restraints

Justin Lemkul jalemkul at vt.edu
Sat May 16 23:05:45 CEST 2015

On 5/16/15 8:13 AM, Ming Tang wrote:
> Dear all,
> I want to minimize my system to relax the solvent with the positions of heavy atoms within the protein restrained. I searched the archives and got the idea that I need to put something like this in topology:
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> But I still have no idea how to get the heavy atoms restrained. Could anybody tell me how to do this?

pdb2gmx does this automatically for you.  It writes posre.itp, which specifies 
heavy atom restraints.  It's controlled by a similar #ifdef block.

> I want to use gromos54a7 ff to simulate my collagen. As Justin suggested, I need to study the original paper "Definition and testing of the GROMOS force-field versions 54A7 and 54B7" to write my .mdp file. In the paper it says,
> 1.      Each system was energy minimised to relax the solvent with the positions of the heavy atoms within the protein and RNA restrained.
> 2.      All solute atom positions were restrained to their positions in the initial structure through a harmonic potential energy term with force constant of 2.5 9 104 kJ mol-1 nm-2.
> Could anybody tell me how to restrain the heavy atoms of protein, and how to get the solute atom positions restrained with a harmonic potential energy term with a certain constant?

This is what posre.itp does.

Also note that you don't necessarily have to follow that protocol exactly; my 
general advice for proper use of force fields is about proper nonbonded setup. 
Preparation of a system often depends on what the system is and if there are any 
special considerations.  For a simple protein system, it's pretty hard to break 
things.  I don't see much benefit in restraining atoms during minimization, though.



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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