[gmx-users] mutation FE calculation with oplsaa

[Maik Goette]

Sure it actually is a bit of work, but:

1. You learn about how FF files are build up
2. You learn about scripting, while doing that stuff.

Probably it's harder for the guys to code that into GROMACS, than for 
you to write a script parsing the files and building your entries....

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


friendli wrote:
> 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>
> Message-ID:
>     <bc2c99750805281433j2af26c8fw7b6158bc6da7a74f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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
> 
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