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

From: Carlos Simmerling <>
Date: Fri, 10 Aug 2007 11:55:02 -0400

you could still use lestemp0 but set the coupling constant to a very
high value for the rest of the system and small for the LES part.

On 8/10/07, Michael Lerner <> wrote:
> 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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Aug 12 2007 - 06:07:51 PDT
Custom Search