[gmx-users] Tricky implementation of REST in GROMACS 4.6.5

Justin Lemkul jalemkul at vt.edu
Tue Nov 18 20:15:50 CET 2014

On 11/18/14 10:44 AM, Carlo Martinotti wrote:
> I'm trying to run a hamiltonian REMD simulation at constant temperature, but i have problems installing plumed with hrex as suggested by Bussi ( https://groups.google.com/forum/#!msg/plumed-users/ROngJ1UyfHI/-nlna83yTy0J ).
> The thing that i was thinking so is to prepare one topology for every replica with pertrurbed values of bonds, lenght, dihedral, charges etc, then make individual tpr files and then run the simulation with multidir and replex.
> The problem is that if i keep the temperature 300K for every replica, gromacs tells me that there is nothing to exchange and the simulation dies.
> So i was wondering, as gromacs needs different temperatures for starting the simulations, is it acceptable to "trick him" introducing for every replica a slightly different temperature (i have to run 32 replicas, i was thinking to run the first replica with unperturbed hamiltonian at 300K and then increment by 0.1 K every replica) ? Would this perturbation affect the exchange probability of 2 replicas significantly?
> Thank you in advance for your time!

I think it makes more sense to simply make use of the free energy code in this 
case to do the HREX.  You can define any number of lambda states for scaling of 
LJ, Coulombic, bonded, etc. interactions and simply define each replica to be 
one of those lambda states.  The replica exchange code works fine when you 
define different lambda states, even at the same temperature.



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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