Dear Tsjerk
Thanks for your right suggestion. It works successfully
for dna-protein complex simulation. i want to ask one more thing , can I use
parameter file for energy minimisation which i have used for membrane
protein simulation or can u suggest me what changes I have to make in
parameter file to use for dna- protein complex simulation.
the parameter file like this-
cpp = /usr/bin/cpp
define = -DPOSRE_PROTEIN
constraints = none
integrator = steep
dt = 0.002
nsteps = 10000
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.0001
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
Specially where i have apply position restrain?
Thanking you
Nitu sharma
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