[gmx-developers] turning charges on/off

David Mobley dmobley at gmail.com
Tue Oct 24 17:17:11 CEST 2006


> > 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.
> No problem for me.
> > (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).
> Not an issue since I don't need the free energy.

OK. Although it probably also does contribute to the total energy, but
this doesn't matter for me, since I'm only interested in the free
energy. :) Probably worth thinking carefully about, though.

> Thanks for the insight. So far it seems that the FEP code will suit my
> purpose, but I will probably have to adapt it so that only certain
> tagged molecules will have a lambda=1 and the rest will have lambda=0.
> That doesn't sound unreasonable eh?

I think the easy way to do that would be with the topology alone: Make
everything in the topology have the same A and B state except the
"tagged molecules"; those will then be the only things that change as
a function of lambda. That's what I normally do too.


> --
> \ Jason de Joannis  \
> \ Emory University  \
>  \ jdejoan at emory.edu \
>   \ 404-402-1332      \
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