[gmx-users] mutation FE calculation with oplsaa

[friendli]

David,

Thanks very much for the explanation. it is quite helpful for me.

Maybe I can suggest the developer to make the definition of only B state plausible. It is quite a tough job to identify parameters of each mutated atom especially in oplsaa, at least for a newbie like me. and if only B is needed to change, the life will be a bit simpler.  
 
LQ

Message: 2
Date: Wed, 28 May 2008 14:33:08 -0700
From: "David Mobley" <dmobley at gmail.com>
Subject: Re: [gmx-users] mutation FE calculation with oplsaa
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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	<bc2c99750805281433j2af26c8fw7b6158bc6da7a74f at mail.gmail.com>
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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