Dear all
I have to apply only Hydrogen molecule will be relax during energy minimization of protein molecule. can anyone have idea about what short of changes I have to make in em.mdp file to allow only hydrogen molecule is relaxable during energy minimisation? my em.mdp file like this- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.001 nsteps = 100 ; ; Energy minimizing stuff ; emtol = 10 emstep = 0.01 nstcgsteep = 1000 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Thanks a lot in advance. Nitu sharma.
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