[gmx-users] decoupling charge while maintaining intramolecular potentials

[chris.neale at utoronto.ca]

Hello,

I am a new user of the free energy code. I am somewhat confused  
regarding the method that should be applied to decouple the long range  
interactions of the solvent from the solute while still maintaining  
intramolecular long-range interactions for the solute.

I was able to find some information in this thread:
http://www.gromacs.org/pipermail/gmx-developers/2006-January/001498.html
but it is still unclear to me.

I have reproduced the methane and tip3p energies of solvation based on  
the tutorial that is on the gromacs wiki. In this case, I simply  
assigned new charge values of 0 in the B state without making any  
special considerations for intramolecular O-H values. However, tip3p  
is rigid and perhaps maintaining the intramolecular q-q and LJ  
components is not essential in this case.

Here are the questions that I am currently struggling to answer:

1. Is it necessary to maintain the intramolecular long-range  
interactions for the solute while decoupling LJ or charge? If not  
absolutely required, does it affect the rate of convergence?

2. Is this already handled by the free-energy code?

3. If not, how might one go about doing this? My confusion with some  
additional [ pairs ] entry is how gromacs would get the right  
combination for lambda=0 and lambda=1 (not to mention intermediate  
states). It seems to me that I would need to create different .itp  
files for each lambda value that have a [ pairs ] section with  
specially calculated values such that this unique pairs contribution  
adds with the contribution from A*(1-lambda)+B*lambda to yield a  
complete intramolecular component. Does this sound correct?

I have seen this applied in Michael Shirts excellent paper from 2003  
and 2005, so I know that there was at least some thought to including  
the ability to do this into the main distribution line of gromacs, but  
that it was not available in v3.1.

Thank you,
Chris.