[gmx-users] Split pmf

[Петр Попов]

2010/10/4 Jochen Hub <jochen at xray.bmc.uu.se>

>  On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote:
>
>> Hello, dears gmx-users!
>>
>> I posted a message, but didn't get a response, it was my first one, so may
>> be I did something wrong. Anyway, here it is:
>>
>> I've already run md and got pmf and it's correct. But I want to get not
>> just a pmf of total force, but several profiles each of which corresponds to
>> the different components. For example, one pmf - protein-protein
>> interactions, another - protein-solvent interactions. Or another, one pmf
>> corresponds to electrostatic, another to VdW etc.
>> Should I change a program's code? If so, tell me please in what exactly
>> program?
>> Or may be gromacs have similar functions? Or is the another way to split
>> pmf?
>>
> Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate through
> aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy file to
> decompose the potential (that is the enthalpic contribution to the PMF) into
> solute-water, solute-protein interactions, etc. You would have to make a tpr
> file with different energy groups and then do a rerun. Note that we do not
> decompose the mean force with that procedure though.
>
> I hope this helps.
>
> Cheers,
>
> Jochen
>
>
>
>
>> Thank you for your attention!
>>
>>
>>
>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational and Systems Biology
> Dept. of Cell&  Molecular Biology
> Uppsala University. Box 596, 75124 Uppsala, Sweden.
> Phone: +46-18-4715056 Fax: +46-18-511755
> http://xray.bmc.uu.se/~jochen/index.html<http://xray.bmc.uu.se/%7Ejochen/index.html>
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Thank you for your response and for the article!
I think it is what I want. But could you explain it more detailed? I mean,
how did you decompose the potential?
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