[gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

[Devashish_Das]

Hello All,

Presently we are working in generating dihedral drivers for AIB dipeptide
in gromacs. We would like to create energy contour maps for different phi,
psi angle for AIB in gromacs. We are unable to create the correct energy
map vs phi/psi angle of AIB dipeptide during energy minimization step in
Gromacs.

Our MDP:
#============================================================
; Parameters describing what to do, when to stop and what to save
integrator = cg
emtol = 1.0
emstep            = 0.01
nsteps = 50000
#============================================================

We retraining the dihedral angles using the following method:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints (*Is this
the correct way to do this?*)

As clarified Dr Justin Lemkul in a private mail, we need to do the
following:

* The 2-D energy surface requires several steps.  You need to
assign dihedral restraints in the topology and relevant .mdp options, and
minimize the structures with those restrained phi/psi pairs.  You then need
to deactivate the restraints and use mdrun -rerun to recompute the energy
of the minimized conformation to eliminate the contribution from the
restraint potential
(http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
<http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>).  Then
you need to offset the surface to the global minimum (done completely
outside GROMACS)*

But we are having following trouble:

a)  "*You then need to deactivate the restraints and use mdrun -rerun to
recompute the energy of the minimized conformation to eliminate the
contribution from the restraint potential*". How to do this? Which .mdp
file to be used for *mdrun -rerun*?

b)  "Then you need to offset the surface to the global minimum (done
completely outside GROMACS)". Can you provide the required tool name?


Regards,

Devashish Das

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