[gmx-users] energy minization mdp
jalemkul at vt.edu
Sat Jul 29 01:16:42 CEST 2017
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
> 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.
Then specify "define = -DPOSRES_BB" in the .mdp 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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