[gmx-users] Free energy calculation: merge the topology of 2 molecules

[Dejun Lin]

Hi all,

I'm trying to set-up a free energy calculation where a molecule has +2
charge in it's native state (state A) and no charge in the mutant (state
B). Since the molecule has net +2 charge, I have to add counter-ions to
neutralize the system in state A. But in order to transform it to state B
and still maintain a neutral system, the counter-ions have to be
transformed too. I tried only transforming only the target molecule not the
ions but the simulation crashes very quickly.

I searched the gmx-users archives and found some suggestion about merging
the topology definition of ions into that of the molecule under one
[moleculetype] section. I tried that but mdrun warned me with tons of
"inconsistent shift":

There were 2 inconsistent shifts. Check your topology
There were 18 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
There were 12 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
...

and the simulation can't be run in parallel because mdrun would just quick
and complain about not being able to do domain decomposition:

There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 29.6188 nm

I guess the issue is Gromacs thinks those counter-ions belongs chemically
to the target molecule although they are actually not in close proximity in
space, which mess up the DD. partition.

I wonder if there's a way to get around that.

Thanks,
Dejun