AMBER Archive (2004)

Subject: Re: AMBER: ntt parameter

From: David Smith (
Date: Thu Dec 02 2004 - 04:30:01 CST

Dear all,

> It would not generally make good physical sense to use ntt=3 with explicit
> water, but there might be situations where you would want to do that.

I know it is quite an involved issue but if this is really the opinion
of the AMBER developers then it might be prudent to add a remark to this
effect in the "DNA polyA-polyT Decamer" tutorial. This is a really nice
tutorial and I believe that most new users will use this to get a feel
for what is sensible to do with AMBER. However, my reading of this
tutorial left me with quite a different impression regarding ntt=3 and
explicit water:

Specifically, the following text threw me off the track a bit.


5.1.5) Molecular Dynamics (heating) with restraints on the solute

"...Prior to AMBER 8 the recommended method for maintaining temperature
was to use the Berendsen thermostat (NTT=1). This method is not very
efficient at ensuring the temperature remains even across the system and
so one would typically have to use NMR restraints in order to ensure
that the heating occurred very gradually over a timescale of about 20
ps. This was essential in order to avoid problems with hot solvent cold
solute etc. AMBER 8 now supports the new Langevin temperature
equilibration scheme (NTT=3) which is significantly better at
maintaining and equalising the system temperature."

Note that this is in the context of equilibrating in explicit solvent.
NTT=3 is also used in the production example of A-DNA.

Please don't take this mail the wrong way but it seems to me that
beginners and semi-experienced users alike could take the information in
this tutorial to mean that NTT=3 is a good idea in explicit solvent. If
it really isn't then it may be helpful to add a comment in the tutorial.

Just my $0.02.



Dr. David Smith
Division of Organic Chemistry and Biochemistry
Rudjer Boskovic Institute
Bijenicka 54
10002 Zagreb, Croatia
tel: +385-1-4561252
fax: +385-1-4561118

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to