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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