[gmx-users] energy minization mdp

Mohammad Zahidul Hossain Khan za.parash at gmail.com
Fri Jul 28 20:54:37 CEST 2017

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.


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*

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