AMBER Archive (2005)

Subject: RE: AMBER:

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Mar 13 2005 - 18:29:08 CST

> On Wed, Mar 09, 2005, Priti Hansia wrote:
> >
> > I want to follow the femtosecond dynamics of macromolecular
> hydration by
> > MD simulation. Experimentally, a femtosecond excitation is
> given to the
> > solute which creates a dipole. This dipole gives rise to an
> instantaneous
> > electric field on the solvent molecules. The interaction of solvent
> > permanent dipoles with the electric field is studied to get
> the solvation
> > time correlation function. This has been studied experimentally on
> > proteins which has a TRP residue on its surface. This
> residue is excited
> > with a femtosecond excitation in the experiment.
> >
> > Now, if I want to follow this with MD simulation, how do I excite or
> > perturb the TRP residue ? Has anybody done this kind of
> studies ? Please
> > help.
>
> You could look at this paper:
>
> %A R.C. Walker
> %A M.M. deSouza
> %A I.P. Mercer
> %A I.R. Gould
> %A D.R. Klug
> %T Large and Fast Relaxations inside a Protein: Calculation
> and Measurement of
> Reorganization Energies in Alcohol Dehydrogenase
> %J J. Phys. Chem. B
> %V 106
> %P 11658-11665
> %D 2002

You might also want to check this paper and the references within:

Byung Moon Cho, Ross C. Walker, Halima Amer, Ian Mercer, David R. Klug, and
Ian R. Gould, J Phys Chem B, 2005, ASAP Mar 2nd.

http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0470748.html

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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