[gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?

Sai Kumar Ramadugu sramadugu at gmail.com
Sun May 6 01:27:57 CEST 2012

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

I have attached the dihedral energy vs dihedral angle curve.

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