Hamiltonian replica exchange

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Is Hamiltonian replica exchange implemented in all gromacs version, and if I want to run Hamiltonian replica exchange only using gromacs without plumed is it possible?

Thanks

2

As of yet, no.

3

Dear all,

I am trying to compute a binding energy using alchemical transformation and following this tutorial
http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
I have found that the use of Hamiltonian Replica Exchange (HREX) can considerably improve the sampling. The command line they suggest (on GROMACS2016) is:

mdrun -multidir lambda.*/PROD/ -s prod.tpr -deffnm prod -replex 1000 -nex 1000000

and does not include plumed. I tried to run it on my system and I am getting errors that I cannot solve. So I was wondering: is this wrong or is actually possible to run HREX without plumed?

Thank you very much for your time,
Damiano