[gmx-developers] turning charges on/off

Jason de Joannis jdejoan at emory.edu
Fri Oct 20 23:48:31 CEST 2006

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>> If it's just a change, then that might be painless, but if you're 
>> changing the number of charges, as you imply above, then things 
>> might be messy. Better would be to define all the sites originally, 
>> and zero the charges for whatever isn't needed at a given step.
> Yes, that sounds good. You probably want to define two topologies, an 
> A and a B state like in FEP calculations. The you turn off the FEP and
> do your algorithm.
I will look into that. It would be great if I could use the FEP code to 
turn molecules on and off.
>  Are you planning to implement constant pH simulations?
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.

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

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