[gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?

[Mark Abraham]

On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote:
> 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.

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.

>
> _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?

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.

Mark

>
> I have attached the dihedral energy vs dihedral angle curve.
>
>
> Regards
> Sai
>
>
>

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