AMBER Archive (2004)

Subject: Re: AMBER: MD & running time

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Jun 23 2004 - 17:25:27 CDT

Folks -
I may be all wet on this, but I quickly perused the code, and it looks to me
like all the pmemd's, and sander 6, 7, and 8 all do basically the same thing
with ntx 5 vs. ntx 7, which is to ignore &ewald box length and angle input
if ntx is 7. This is actually not all that useful (since you can just leave
the &ewald input out), so (presumably) documentation of ntx 7 was dropped in
sander 7/8, but not the functionality. An attempt is always made to get box
info from the bottom of inpcrd/rest if periodic boundary conditions are in
effect. I guess I would read the mdout to be sure of what is happening...
David, I leave it to you to let me know if I am confused ;-)
Regards - Bob Duke

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, June 23, 2004 5:02 PM
Subject: Re: AMBER: MD & running time

> On Wed, Jun 23, 2004, Kristina Furse wrote:
> > I was under the impression that the information Ross Walker gave (below)
about
> > ntx=5 and ntx=7 in Amber 8 was also true for Amber 7--basically that
they do
> > the same thing and ntx=7 was there for backwards compatibility--but not
for
> > Amber 6, where they have different definitions. If this is not true,
then I
> > am in big trouble...
>
> I think you are correct: these options are different in Amber 6. Starting
> with Amber 7, the box information is always read from the restart file for
> periodic systems, if it exists there.
>
> ...dac
>
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