[gmx-developers] turning charges on/off

Jason de Joannis jdejoan at emory.edu
Tue Oct 24 18:29:45 CEST 2006

Quoting David Mobley <dmobley at gmail.com>:

> Jason,
>> > 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.
I'm not sure what you mean. Anyways, all of the molecules I intend to 
use will all have neutral charges, so I shouldn't have to think about 
pme kicking in with an automatic charge-neutralization cloud.
>> 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.
I want more degrees of freedom than that though. I will want a separate 
lambda for each lipid in the system. In other words, replace the single 
parameter with an array of parameters. That way my system composition 
is dynamic. It could be 25% A at one moment and later on shift to 50 or 
75% A.

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

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