Aw: Re: [gmx-users] How to calculate enthalpy

[lloyd riggs]

 

I thought about this reguaring solvation energy.  If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2.  I assume you could do some extreemly accurate solvation energy calculations this way, but the guassians for say 10-20 parallel runs of the same system would be much greater than say a protein-protein interaction.  I am sure solvent models would have to be good as well, but may allow you to do what you wished, however I would make sure through others first, and I do not know what you wished to do completly.

 

Stephan Watkins

Gesendet: Montag, 15. Juli 2013 um 19:25 Uhr
Von: "lloyd riggs" <lloyd.ri...@gmx.ch>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Aw: Re: [gmx-users] How to calculate enthalpy

Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)?  And the energy of the internal structural hydrogen bonds that were disrupted?  Assuming no acidic enviornment where electrons are involved...means of coarse...

 

Gesendet: Montag, 15. Juli 2013 um 10:34 Uhr
Von: pooja_gu...@nccs.res.in
An: vvcha...@gmail.com, "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] How to calculate enthalpy

Thanks Vitaly

but how??

let's say the difference between unfolded to folded protein is 100 water
molecules. What is the correct procedure to calculate (theoretically) the
entrapy correspond to single water molecule for stabilizing/destabilizing
the protein.

help me

> Sure, you can.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 15, 2013 at 8:38 AM, <pooja_gu...@nccs.res.in> wrote:
>
>> Hi
>>
>> I want calculate the enthalpy of water molecule corresponding to protein
>> folded and unfolded state.
>> How much a single water molecule (enthalpy and free energy) contribute
>> in
>> folding ?
>> Can we calculate enthapy from g_energy?
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists