Re: NTT=5?

From: David Case <>
Date: Mon 29 Apr 2002 22:32:20 -0700

On Mon, Apr 29, 2002, Jung-Hsing Lin wrote:
> I think many people have noticed that in sander of Amber 6 and 7, the NTT
> options have been restricted to NTT=0, 1, and 4. This probably means now
> AMBER doesn't encourage people to use independent thermostats for
> couplings to solute and solvent. I can understand that multiple
> thermostats are intuitively artificial, but I thought such an approach was
> meant to remedy the problem of "hot solvent, cold solute" or
> "inhomogeneous temperature gradient" artifacts. I know that a good source
> of related discussions can be found in the article by Harvey et al. J.
> Comp. Chem., 19, 726-740 (1998) "The Flying Ice Cube ....", but it is
> still not clear to me if the problem with NTT=1 (single thermostat) can be
> remedied by removing center of mass motions alone (probably with the
> particle mesh Ewald method).
> ...Could anyone provide me
> with the "insider information" for the reason why other NTT options have
> been turned off....

The general recommendation now is to set ntt=0 during production periods,
only using thermostats to establish a target temperature during
equilibration. With the default Ewald scheme, energy conservation should be
good enough to alow the thermostats to be turned off (for all but the
longest runs); alternatively, setting tautp to a fairly large value (like
5.0) also can avoid the "hot solvent/cold solute" problem.

The old ntt=5 scheme probably could have been kept if we had had a better
scheme for deciding what was "solute" and what was "solvent". Earlier Amber
codes progressively became more and more complex and arcane, with several
different schemes and variables being used to try to identify "solvent", but
none of them very good for anything but TIP3 water.

We are working on a revamped scheme to identify groups of atoms (no more
rgroup()!). I had hoped this would be ready for Amber7, but it was not.
Once that is in place, it should be much easier to go back and insert
separate temperature baths if one wants. As with many things, the code
itself is trivial -- it's designing the user interface, and then
documenting that, that always seems to take more time than one can possibly

Others on the list may want to chime in here as well.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Mon Apr 29 2002 - 22:32:20 PDT
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