[gmx-users] mutation FE calculation with oplsaa

[Qiang Li]

Dear all users,

1,
I am modifying the .top file for mutation free energy calculation(A->B), so
I need the provide the parameters of structure A and B in [bonds], [angles],
[dihedrals].
Is it possible for me to provide only the parameters of B but le the grompp
using the default parametes of initial structure A?

I know the A parameters will be copied to B if parameters of B is not
explicitly defined in .top. IS that means I must explicitly define both A
and B at the same time?
I ask it since I find in OPLSAA force field the .top file does not contain
paramters of [bonds], [angles],... but only the atome numbers and function
types.

2,
When comparing the solvation free energy tutorial from
http://md.chem.rug.nl and
the wiki(Dillgroup), I get confused at the definition of solvation free
energy.
In the former, dG=dG1(in vacuo)-dG2(in water); however, in the latter it
seems only calculating the dG2(in water) gives excellent result compared to
expt.
Did I misunderstand anything here?

thanks a lot

LQin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080524/5990569e/attachment.html>