[gmx-users] energy minization mdp
Mohammad Zahidul Hossain Khan
za.parash at gmail.com
Sat Jul 29 23:02:22 CEST 2017
Thank you very much. It is working now.
On Fri, Jul 28, 2017 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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"
> 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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*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
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