AMBER Archive (2005)

Subject: AMBER: how to excite a single residue ?

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Wed Mar 09 2005 - 22:28:24 CST

Hi,

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.

Regards,
-Priti

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