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On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote:
<blockquote
cite="mid:CAO6uzQXw13tvNr6xNaUXLh=446eFgT3QiE7sZs+bS9hE7MJKOg@mail.gmail.com"
type="cite">Dear Gromacs Users,
<div><br>
</div>
<div>I am trying to plot the Ryckaert-Bellemans energy for
rotating the chi1 dihedral of glutamate in protein.</div>
<div>I tried to change the ch1 dihedral from 0-360 degrees at
increments of 1 degree and saved the pdbs. Then I used the pdb's
to obtain the corresponding gro files and a single topology
file.</div>
<div>I used opls force field and no water and a 0 step
minimization.</div>
</blockquote>
<br>
If your GROMACS version is up to date, then grompp will have warned
you that this is not the best procedure for measuring energies of
input configurations. Use mdrun -rerun and a fake trajectory
constructed from your sets of coordinates.<br>
<br>
<blockquote
cite="mid:CAO6uzQXw13tvNr6xNaUXLh=446eFgT3QiE7sZs+bS9hE7MJKOg@mail.gmail.com"
type="cite">
<div><br>
</div>
<div><u>My em.mdp file:</u></div>
<div><u><br>
</u></div>
<div>
<div>cpp = /usr/bin/cpp</div>
<div>define = -DFLEXIBLE</div>
<div>integrator = steep</div>
<div>nsteps = 0</div>
<div>constraints = none</div>
<div>emtol = 1000.0</div>
<div>emstep = 0.01</div>
<div>nstcomm = 1</div>
<div>ns_type = grid</div>
<div>nstlist = 1</div>
<div>rlist = 0</div>
<div>rcoulomb = 0</div>
<div>rvdw = 0</div>
<div>Tcoupl = no</div>
<div>Pcoupl = no</div>
<div>gen_vel = no</div>
<div>nstxout = 1</div>
<div>pbc = no</div>
<div>;energy groups</div>
<div>energygrps = Protein </div>
</div>
<div><br>
</div>
<div>After the minimization, when I plot the dihedral energy vs
dihedral angle, I do not get a symmetrical curve.</div>
<div>After careful observation of the gro files that I obtained
using pdb2gmx, the 0-180 values are not exactly same as -180-0
degrees or 180-360 degrees.</div>
<div>Is it because of the slightly different values of the
dihedral 0-180 and 180-360 that I'm not getting a symmetrical
curve or am I doing something wrong?</div>
</blockquote>
<br>
Only if you vary the dihedral of interest and then follow the above
procedure while holding the other internal degrees of freedom fixed
will you observe the variation solely due to this RB dihedral. You
can plot this more easily from the functional form defined in the
force field files, of course.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAO6uzQXw13tvNr6xNaUXLh=446eFgT3QiE7sZs+bS9hE7MJKOg@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>I have attached the dihedral energy vs dihedral angle curve.</div>
<div><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div>Sai</div>
<div><br>
</div>
<br>
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<br>
</blockquote>
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