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><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><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>