[gmx-users] mutation FE calculation with oplsaa

[friendli]

Thanks Maik for the comments.

Maik Goette wrote:
> 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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