[gmx-users] problem during simulation of dna-protein complex

[nitu sharma]

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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