AMBER Archive (2004)

Subject: Re: AMBER: Hot solvent/cold solute reference

From: Stef (
Date: Mon Oct 11 2004 - 11:41:10 CDT

Le lundi 11 octobre 2004 à 15:16 +0200, Andreas Svrcek-Seiler a écrit :
> Hi,
> > After spending some time on searching the reference, i'm asking here ;-(
> > So far, i've found :
> > Harvey et al. J. Comp. Chem., 19, 726-740 (1998) "The Flying Ice
> > Cube ...."
> > Is it correct ?
> ... why shouldn't this be correct ?

I mean : is the citation the primarily one, i know the hot solvent/cold
solute is real ;-)

It is mentionned many times in the manual (at least on version 6.0, 7.0
and 8.0) and on tutorials (for instance on was mentioned but is now
replaced by polyA-polyT_new -indeed very informative, nice job !) but i
have not been able to find a reference talking explicitly of 'hot
solvant/cold solute'.

The citation "Harvey et al. J. Comp. Chem., 19, 726-740 (1998) "The
Flying Ice Cube ...." mentions hotspots, but is basically addressing
another problem (movement of the entire system.

I was just trying to find if there is a previous citation mentionning
this explicitly since it seems anterior to this publication. So far my
research have given me this 'feeling' :
'it must be something known by everyone and sometimes refered in a paper
(but not linked to any citation), but no specific study has addressed
the problem closely, so there is no 'real' reference. It is a kind of
universal knowledge ;-).


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