[gmx-users] mutation FE calculation with oplsaa

[David Mobley]

Qiang,

I can help somewhat, I think.

> 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?

No, it's not.

> 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?

If you want to specify B parameters, you must specify A parameters.
You can define A only, or A and B, but not B only.

> 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?

In the Dill group example, it is the Lennard-Jones component of the
solvation free energy of methane. Since methane has no intramolecular
Lennard-Jones interactions (due to exclusions) the vacuum component
would be zero.

So, yes,you're right, dG=dG(in vacuo)-dG(in water), but in the methane
example dG(in vacuo)=0 (at least for LJ).

David
> thanks a lot
>
> LQin
>
> _______________________________________________
>  gmx-users mailing list    gmx-users at gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
>  www interface or send it to gmx-users-request at gromacs.org.
>  Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>