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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