Re: amber-developers: cvs amber9

From: David A. Case <>
Date: Wed, 20 Apr 2005 10:43:11 -0700

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
> 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
> 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
> changes through cvs. Mike has changed my account name to wuxw and it
> perfect.

Thanks....I'll take a look at this when I have a chance. Is there any
paper on this, besides CPL 381: 512 (2003)?


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Apr 05 2006 - 23:49:57 PDT
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