[gmx-users] problem during energy minimisation to allow only hydrogen molecule to relax

[nitu sharma]

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090706/bdd5267e/attachment.html>