Dear all <br><br><br> I have to apply only Hydrogen molecule will be relax during energy minimization of protein molecule.<br><br>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?<br>
my em.mdp file like this-<br><br>cpp = /usr/bin/cpp<br>define = -DFLEX_SPC<br>constraints = none<br>integrator = steep<br>dt = 0.001<br>nsteps = 100<br>
<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 10<br>emstep = 0.01<br>nstcgsteep = 1000<br>nstcomm = 1<br>nstlist = 10<br>ns_type = grid<br>
rlist = 1.0<br>rcoulomb = 1.0<br>vdw-type = cut-off<br>rvdw = 1.0<br>coulombtype = PME<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>
comm-mode = Linear<br>pbc = XYZ<br>Thanks a lot in advance.<br><font color="#888888"><br>Nitu sharma.<br>
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