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

Carlo Martinotti carlo.martinotti at studenti.unimi.it
Tue Nov 18 16:44:48 CET 2014

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!

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