Hi,
> I used the following protocol from the example in tutorial A9.
Thats looks fine to me.
> Since I dont have any atoms or charges to be added, I dont have step3. Am
> I right in assuming this?
yes, in this case that third step would be unneccesary.
> The values are close to your JCC paper titled "Soft-core Potentials in
...
> Further, my values are shifted in sign for step 1 and step 2.
> Am I doing something wrong here?
Well, if you reproduce our values, then everything should be correct.
TIP3P vs. TIP4PEw may make a small difference. The sign comes from the
fact that you are simulating the removal of Cl- from water, while in our
paper we report solvation free energies, which correspond to the reverse
process. My raw numbers had the same signs as yours.
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Jan 13 2012 - 05:30:04 PST
