Hi Abhishek,
'total' is the solvation free energy of the solute. 'O' and 'H1' are the contributions to this from the O and H1 atom types of the solvent (TIP3P). For almost all purposes, 'total' is the number that is of interest.
Tyler
On 2013-04-20, at 6:00 PM, Abhishek Mukhopadhyay wrote:
> Thank you for sharing the tutorial, that was very helpful. I have one more
> doubt though. I tried adding TIP3P using the TP3.mdl file. Now when I use
> rism3d.snglpnt with the flag --polarDecomp I get the energies for total, O
> and H1. Which one amongst these is/are the solvation free energy for just
> the solute?
>
> Thanks,
> Abhishek
>
> On Fri, Apr 19, 2013 at 6:34 PM, tluchko <tluchko.rutgers.edu> wrote:
>
>> Hi Abhishek,
>>
>> I would recommend starting with the user's manual to become acquainted
>> with method and the ways to access the method.
>>
>> There is no tutorial on the Amber website yet, but Daniel Sindhikara has
>> created one for 3D-RISM and his associated Placevent method:
>>
>>
>> http://dansindhikara.com/Tutorials/Entries/2012/1/1_Using_3D-RISM_and_PLACEVENT.html
>>
>> Tyler
>>
>> On 04/19/2013 06:10 PM, Abhishek Mukhopadhyay wrote:
>>> Hi Tyler,
>>>
>>> Thanks for your prompt response. I am a graduate student working for Dr.
>>> Alexey Onufriev. We are trying to come up with an improvement over Gen
>> Born
>>> by adding a asymmetric response of the solvent into the formalism. In
>> this
>>> regard we have had some success and we'd like to compare with other
>> methods
>>> that are out there. RISM incorporates this asymmetry and that's why it's
>> a
>>> good candidate to compare with.
>>>
>>> Getting back to what you suggested. Is there a tutorial for finding these
>>> solvation energies using RISM. If not what are the steps the solvation
>>> energies? Do I need to solvate the molecule first and equilibrate it?
>> Does
>>> this method directly separates out the energy terms for the solvent?
>>>
>>> Kindly take me through this as I have never used this formalism and not
>>> really proficient in AMBER.
>>>
>>> Thanks,
>>> Abhishek
>>>
>>>
>>> On Fri, Apr 19, 2013 at 5:02 PM, tluchko <tluchko.rutgers.edu> wrote:
>>>
>>>> The easiest way to run 3D-RISM (and get the solvation free energy) is
>>>> with rism3d.snglpnt. The solvation free energy is always computed with
>>>> a range of other thermodynamic data and output in a table. The row
>>>> starting with 'rism_exchem' gives the total excess chemical potential of
>>>> solvation (solvation free energy) in the first column. The remaining
>>>> columns give contributions from the various components of your solvent.
>>>> A key for this table is printed at the top of your run.
>>>>
>>>> This is computed from a single solution to the 3D-RISM equation, which
>>>> is described in the AmberTools manual (Section 9.1.2). You can further
>>>> decompose the solvation free energy into polar and non-polar
>>>> contributions using the --polarDecomp flag.
>>>>
>>>> Tyler
>>>>
>>>> On 04/19/2013 04:36 PM, Abhishek Mukhopadhyay wrote:
>>>>> Hi,
>>>>> Is there a direct way to compute free energy of hydration using
>> 3D-RISM?
>>>> If
>>>>> not, do I need to do Thermodynamic integration? Please help.
>>>>>
>>>>> Thanks,
>>>>> A.M
>>>>> _______________________________________________
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> --
>>>> ________________________________________________________________
>>>> Tyler Luchko
>>>> Postdoctoral Associate
>>>> Case Group
>>>> BioMaPS Institute
>>>> Rutgers University
>>>> Piscataway, New Jersey
>>>> tluchko.rutgers.edu
>>>> 848-445-5239
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>
>> --
>> ________________________________________________________________
>> Tyler Luchko
>> Postdoctoral Associate
>> Case Group
>> BioMaPS Institute
>> Rutgers University
>> Piscataway, New Jersey
>> tluchko.rutgers.edu
>> 848-445-5239
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
848-445-5239
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Received on Sat Apr 20 2013 - 15:30:03 PDT
