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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>>> AMBER.ambermd.org
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>>>
>>
>> --
>> ________________________________________________________________
>> 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
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Received on Fri Apr 19 2013 - 16:00:03 PDT
