AMBER Archive (2007)

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

From: Michael Lerner (mlerner_at_umich.edu)
Date: Fri Aug 10 2007 - 16:35:38 CDT


Dr. Simmerling-

In my initial runs, I didn't play around much with the coupling
constant. I'm probably missing something obvious in the manual, but I
didn't see a way to set different coupling constants. Is there a
setting like "tautples" that I missed?

Thank you,

-Michael

On 8/10/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> 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 <mlerner_at_umich.edu> 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
> > http://www.umich.edu/~mlerner
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