Hi,
> When I was going through your tutorial, using softcore potential, you dont
> need to have same number of atoms that are undergoing the transformation.
> But in my case I have only one atom/ion in the transformation. How can I
> achieve the transformation of a neutral atom to K+ or Cl-? Should I use
> dummy atoms instead? If so, can you point me how to use the dummy atoms
> for
> the necessary transformation?
> I did not understand how to use/include dummy atoms using ff99SB force
> field.
Hi,
there is no need to use dummy atoms in the type of calculation you plan.
Just set up your system as:
System 1 System 2
Ion + Water just Water
and set scmask in our input files to the Ion residue(s). Make sure all
water molecules have the same coordinates in Systems 1 and 2 or your sim
will halt with an error.
This decouples both the (in this case very dominant) Coulomb as well as
vdW interactions and gives you (with some caveats) the free energy of
solvation.
Check out the Steinbrecher, Joung and Case J. Comp. Chem. paper for an
example using Cl-.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Jan 03 2012 - 13:00:02 PST
