On Mon, Mar 30, 2015 at 8:20 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Mar 29, 2015, FyD wrote:
> >
> > In parm99.dat one can find the following line (i. e. between the
> > improper & vdW sections):
> >
> > HW OW 0000. 0000. 4. flag for fast water
>
> This line mainly defines HW...OW as a "hydrogen bond", which in modern
> parlance means that its LJ terms will be skipped (unless you have compiled
> Amber with the -DHAS_10_12 flag set). I'm guessing that the comment is
> out of
> date.
>
​Unless it's to claim that by skipping the Lennard-Jones calculation for
OW-HW atom types, the calculation speeds up slightly... My first guess was
that at some point in the past it was used to somehow flag waters for
SETTLE treatment instead of SHAKE. But going back to Amber 5, the SETTLE
source code was clearly there, but the HBOND_ACOEF and HBOND_BCOEF arrays
had nothing to do with identifying waters.
(I was working on my own response to this question, but Dave beat me to it
:)).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 30 2015 - 05:31:04 PDT
