Dear Dave,
I test simulations with a water solution on SGI shows ips=1 uses only 6%
more cpu time than ips=2. 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.
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!
Xiongwu
> -----Original Message-----
> From: David A. Case [mailto:case.scripps.edu]
> Sent: Tuesday, April 19, 2005 5:32 PM
> To: amber-developers.scripps.edu
> Subject: Re: amber-developers: cvs amber9
>
>
> On Tue, Apr 19, 2005, Wu, Xiongwu (NIH/NHLBI) wrote:
> >
> > The new results are OK. The different from those of
> wxwsander is because of
> > the bugs in my previous implementation in Amber8.
>
> OK...thanks.
>
> >
> > Your implementation to make vdwmeth=1 work with ips=2 is
> very helpful for
> > comparison between IPS and PME. For both periodic and
> non-periodic systems,
> > ips=1 would be recommended.
>
> I haven't yet done a lot of timings, but I would think that
> ips=2 should be
> computationally more efficient that ips=1, and almost as
> accurate. Do you
> have any experience about this?
>
> >
> > Mike, I don't know how much trouble it would cost to change
> my user name to
> > wuxw or xiongwu.
>
> I'll bug Mike to make this change.
>
> ...thanks!...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
