[gmx-users] problem during energy minimisation to allow only hydrogen molecule to relax
x.periole at rug.nl
Mon Jul 6 09:31:03 CEST 2009
you could use position restrains on the other atoms (non hydrogens) or
use freezing groups.
it seems that your system has a major problem: bad contacts ... check
it prior to EM.
On Jul 6, 2009, at 8:30 AM, nitu sharma wrote:
> 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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