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
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Abhishek Mukhopadhyay
PhD fifth year, Department of Physics
Virginia Tech
Blacksburg, Virginia 24061-0435
phone: ++1-540-250-8369
email: abmukho.vt.edu
url: https://bioinformatics.cs.vt.edu/~abmukho/
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Received on Fri Apr 19 2013 - 15:30:04 PDT
