[gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified

Justin Lemkul jalemkul at vt.edu
Wed Dec 17 14:02:48 CET 2014

On 12/17/14 12:44 AM, Christopher Neale wrote:
> Dear Users:
> I'm trying to induce a protein to unfold and I'd like to use a
> free-energy-like lambda value to specifically weaken only the attractive part
> of the LJ interactions within the protein, while leaving LJ interaction
> between protein and water unmodified. Is there any way to do this in
> gromacs?

If you're just looking to scale the interactions by some scalar value (and not 
multiple points, as in the case of lambda free energy transformations), I would 
do it by using [nonbond_params] to specify scaled protein-protein interactions 
to override what is normally generated by combination rules.  Then the 
protein-water interactions are handled normally but the protein-protein 
interactions are treated by your special parameters.


> I've had some success with the converse approach of using the free energy
> code to strengthen the LJ and coulombic interactions between protein and
> water by removing the grompp errors in the source code when lambda is greater
> than 1, recompiling, then in the .mdp file setting lambda=0 to none and
> lambda=1 to vdw-q and then running at lambda=1.5 with couple-intramol=no. One
> problem with this approach is that when I use couple-intramol=no it kills the
> parallelization due to the exclusions, so a simulation that could previously
> run on 8 cores now maxes out on a single core since domain decomposition is
> impossible on more cores. Another problem is that even though in the
> thermodynamic limit it should be equivalent to weaken one interaction or
> strengthen another, I suspect that I'd see much more rapid unfolding by
> weakening the intramolecular protein attractions than by strengthening the
> protein-water interactions.
> Thank you for your help, Chris.


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


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