[gmx-users] decreased performance with free energy

[David de Sancho]

Hi all
I have been doing some testing for Hamiltonian replica exchange using
Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic
box.
For the modified hamiltonian I have simply modified the water interactions
by generating a typeB atom in the force field ffnonbonded.itp with
different parameters file and then creating a number of tpr files for
different lambda values as defined in the mdp files. The only difference
between mdp files for a simple NVT run and for the HREX runs are the
following lines:

> ; H-REPLEX
> free-energy = yes
> init-lambda-state = 0
> nstdhdl                 = 0
> vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

I have tested for performance in the same machine and compared the standard
NVT run performance (~175 ns/day in 8 cores) with that for the free energy
tpr file (6.2 ns/day).
Is this performance loss what you would expect or are there any immediate
changes you can suggest to improve things? I have found a relatively old
post on this on Gromacs developers (https://redmine.gromacs.org/issues/742),
but I am not sure whether it is the exact same problem.
Thanks,

David