Dear Gromacs Users, I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1 dihedral of glutamate in protein. 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. I used opls force field and no water and a 0 step minimization.
*My em.mdp file:* * * cpp = /usr/bin/cpp define = -DFLEXIBLE integrator = steep nsteps = 0 constraints = none emtol = 1000.0 emstep = 0.01 nstcomm = 1 ns_type = grid nstlist = 1 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no ;energy groups energygrps = Protein After the minimization, when I plot the dihedral energy vs dihedral angle, I do not get a symmetrical curve. 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. 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? I have attached the dihedral energy vs dihedral angle curve. Regards Sai
<<attachment: chi1_gromacs.png>>
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
