AMBER Archive (2004)

Subject: Re: AMBER: non-isotropic pressure scaling

From: Robert Duke (
Date: Wed Mar 24 2004 - 07:44:35 CST

Lubos -
The pmemd released under Amber 8 does support non-isotropic pressure
scaling. It should also give you better performance and scaling than 3.01
on many systems, exact correspondence on virials with sander 8, etc. etc.
It would also be possible to patch pmemd 3.01 or better, 3.1 (which has
better performance and scaling, and is available on the amber web site) to
support this; you would need to look at the code in mdin_ctrl_dat.f90 and
runmd_*.f90, and compare to equivalent code in sander 7 (and do comparison
test runs to be sure you got it right). The non-isotropic scaling
capability is not in pmemd 3.01 - 3.1 because these programs were intended
to be mostly sander 6 compatible, and it did not support non-isotropic
scaling. The feature sets in 3.01-3.1 are described relatively thoroughly
in the release and update notes in the tarball, but they are described as
deltas from sander 6 functionality. Functionality for pmemd 8 is described
in the Amber 8 manual, but as a delta from sander 8 functionality (prevents
two big redundant manual sections).
Regards - Bob Duke

----- Original Message -----
From: "Lubos Vrbka" <>
To: <>
Sent: Wednesday, March 24, 2004 7:38 AM
Subject: AMBER: non-isotropic pressure scaling

> hi guys,
> i'm currently using amber for simulating non-isotropic system
> (interface) under constant pressure conditions. whereas sander (version
> 7) works fine with ntp=2, pmemd doesn't support it yet (version 3.01).
> do any of newer versions of pmemd support this? and if not, is there
> plan to include the support in some of the newer releases? i'd rather
> use pmemd here, because i'm running the jobs on parallel machine and
> pmemd is ~30% faster...
> i was trying to find the full list of pmemd-supported features on net,
> but i wasn't succesful...
> thanks for help,
> --
> Lubos
> _@_"
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

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