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

[Justin Lemkul]

On 3/17/17 1:40 AM, Devashish_Das wrote:
> 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*?
>

Anything that's not energy minimization.  Your topology also should either not 
include the dihedral restraint, or you should extract its contribution from the 
.edr file and subtract it from the total energy of the system.

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

There isn't one.  This is a trivial scripting exercise.  You assemble the 2-D 
matrix of energy values, find the lowest energy, and apply it as a global offset 
to all values.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================