We have implemented in the popular molecular-dynamics software GROMACS the possibility to efficiently run Hamiltonian replica exchange simulations using modified force-fields. In standard GROMACS, this can only be done using free-energy perturbation, which is very expensive. Our tool is very promising because of its flexibility. Indeed, one can easily select a portion of a system that would like to accelerate and only touch that portion, thus avoiding undesired effects such as RNA/protein unfolding. Moreover, the number of required replicas scales only with the number of atoms in the selected portion. We benchmark the method on alanine dipeptide and on an RNA tetraloop. Applications to more complicated systems are on the way.
The implementation is integrated with the open source PLUMED package and will be included in a future release of PLUMED. For the moment, you can just contact us and request a copy of the software or get it here.
This work has been accepted for publication on Molecular Physics, and is available free of charge. The preprint is available at arXiv:1307.5144.