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.
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