[gmx-users] Gromacs Relative Free Energy Calculation Issue

[Hannes Loeffler]

On Wed, 5 Oct 2016 09:28:16 +0000
Guanglin Kuang <guanglin at kth.se> wrote:

> I have also tried alchemistry_setup.py, the resultant files would not
> have this problem and everything runs properly. I think the problem
> may be due to the fact a direct mutation is used with FESetup, namely
> mutate H to O. However, with alchemistry_setup.py, it is indirect
> mutation, namely H to dummy, and dummy to O, separately. This is the
> only difference I found with FESetup and alchemistry_setup.py. The
> mdp files are the same.

As explain in my previous email that in itself is not a problem.  When
you say that alchemistry_setup.py provided a certain mapping I think
that you must have instructed it to do so.