AMBER Archive (2007)

Subject: AMBER: How to couple only one residue to the temperature bath?

From: Michael Lerner (mlerner_at_umich.edu)
Date: Fri Aug 10 2007 - 09:45:10 CDT

Hi,

I'm trying to do some work that is similar to Ota and Agard's
anisotropic thermal diffusion (Ota, N. & Agard, D. A. (2005) J. Mol.
Biol. 351, 345-354.). In this method, only the side-chain atoms of a
particular residue are coupled to the temperature bath. The
temperature coupling is turned off for the rest of the protein, and
one examines how the thermal energy propagates outwards from the
residue of interest. This is a non-equilibrium method that involves
injecting energy into the system throughout the simulation.

Is there an obvious way to do this in AMBER 8 (or AMBER 6)? The
closest I was able to come was to use LES (temp0les in particular) to
couple one residue to a high-temperature bath and the rest of the
protein to a low-temperature bath. This isn't really what I want
because 1) everything is coupled to *some* temperature bath and 2) the
total energy of the system is kept constant.

If there's no built-in way, can someone give me a little guidance in
how I might edit the source code to get what I want? I've looked
through it a bit. It seems that it might be somewhat tricky to mess
around with the temperature couplings, and if I edit the source, I
want to make sure that I don't miss anything.

Thanks in advance,

-michael

P.S. My apologies if the list gets two copies of this. I sent one
yesterday and it didn't go through. I think I sent from an
unsubscribed account, though. 

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner
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