Michael,
there is not, but in runmd.f it is pretty easy to
change the scaling for the LES and non-LES parts.
Are you familiar with the code, or with fortran?
check the parts of runmd that set "scaltp".
Let m eknow if you need more help and I can
point out the lines, can't do it right now.
carlos
On 8/10/07, Michael Lerner <mlerner.umich.edu> wrote:
> 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.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.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
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 12 2007 - 06:07:55 PDT
