[gmx-developers] turning charges on/off

[David Mobley]

Jason,

> No. I am planning on doing mutations between molecular species A and B.
> Our idea is to have duplicate molecules with one on and one off. I know
> how to turn off the Lennard-Jones, but I was worried about the charges.

I am not sure I am *completely* clear on what you are doing, but if
you are just talking about turning molecules on and off, you can
definitely do this with the FEP code. The FEP code works fine with PME
as long as both A and B states have the same net charge, which should
always be the case for you unless the molecules you are
inserting/deleting have different net charges. (In some sense, it
works 'fine' anyway, in that the algorithm works fine, but there would
be a contribution to the free energy due to turning on the netralizing
charge used by PME, which is probably not what you want).

To give you an idea of a "standard" calculation of this sort, I
commonly do hydration free energy calculations where I first turn off
the charges on my molecule in water, then turn off the Lennard-Jones
interactions between the molecule and water, and then turn the charges
back on in vacuum to get a hydration free energy. This works fine with
PME. It sounds somewhat similar to what you are thinking.

On an unrelated note, if you are thinking about making MC moves
between different molecules, you may need to think carefully about
whether the phase space overlap is good enough to get anything
meaningful back. As you're undoubtedly aware, we typically do these
calculations with MD by adding intermediate states (  i.e. states
where the molecule is 1/3 A and 2/3 B, 1/2 A and 1/2 B, 2/3 A and 1/3
B, and so on), as the overlap between the A and B states is generally
poor (different solvent configurations, etc). This would probably show
up in MC with poor acceptance ratios, I suppose.

Best wishes,
David Mobley
UCSF
> --
> \ Jason de Joannis  \
> \ Emory University  \
>   \ jdejoan at emory.edu \
>    \ 404-402-1332      \
>
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>