On Wed, Apr 20, 2005, Wu, Xiongwu (NIH/NHLBI) wrote:
>
> I test simulations with a water solution on SGI shows ips=1 uses only 6%
> more cpu time than ips=2.
I found similar behavior on an itanium system (SGI-Altix: is this what you
used?) I will try some similar tests on Pentiums. But you are probably
correct: it would be generally better to use ips=1 than 2.
I am running some detailed studies on pure water, and on charging free
energies in water, mainly for my own benefit, to see what happens.
> For water systems, ips=1 or ips=2 may not make to
> much difference with cut=10 Angstroms. But for less polar systems like
> lipid, Rich Pastor has shown that ips produces much better properties
like
> surface tension than normal long-range correction(LRC). For argon
fluid, as
> shown in my JCP paper, the density using LRC depends on cutoff distance
up
> to 20 angstroms, while not with ips. In addition, with ips the force is
> continuous at the cutoff boundary and the energy profile is much more
> smoother than that from LRC. This is just my opinion.
You opinion is pretty valuable!
>
> I finish the implementation of SGLD into Amber 9 and have just committed
the
> changes through cvs. Mike has changed my account name to wuxw and it
works
> perfect.
Thanks....I'll take a look at this when I have a chance. Is there any
other
paper on this, besides CPL 381: 512 (2003)?
...regards...dave
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Wed Apr 05 2006 - 23:49:57 PDT
