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. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>* * Skype: parash.khan2* *Cell: +12085967165* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
