[gmx-users] energy minization mdp

[Justin Lemkul]

On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:
> Dear User
> 
> I have protein-ligand system. I have basic idea for energy minimization.mdp
> parameter.
> ;
> integrator = steep
> emtol = 10.0
> emstep = 0.01
> nsteps = 500
> energygrps = Protein OAI
> ;
> nstlist    = 1
> cutoff-scheme = Verlet
> ns_type    = grid
> rlist    = 1.0
> coulombtype    = PME
> rcoulomb    = 1.0
> rvdw    = 1.0
> pbc        = xyz
> 
> but I have not idea how to write the parameter *where all the backbone
> heavy atoms of the protein have to be constrained with an elastic constant
> of 50 kcal /mol Å -2 and the other atoms should be free.*
> 
> Does anyone know how to write elastic constant parameter in energy
> minimization mdp file.
> 

Restraints are a topological construct, not one that is (directly) specified in 
the .mdp file.  Run your protein coordinates (only) through gmx genrestr and 
choose the backbone as the output group.  Specify the desired force constant on 
the command line (make sure to convert your value to kJ mol^-1 nm^-2).  Save the 
new position restraint file to something like "posre_bb.itp" and #include it in 
the topology in the protein's [moleculetype] section, e.g.

#ifdef POSRES_BB
#include "posre_bb.itp"
#endif

Then specify "define = -DPOSRES_BB" in the .mdp file.

-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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