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
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
> >
>
> --
> ________________________________________________________________
> 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
>
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Received on Sat Apr 20 2013 - 15:30:03 PDT
