RE: amber-developers: cvs amber9

From: Wu, Xiongwu \(NIH/NHLBI\) <"Wu,>
Date: Tue, 19 Apr 2005 10:19:42 -0700

Dear David,

The new results are OK. The different from those of wxwsander is because
the bugs in my previous implementation in Amber8.

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
ips=1 would be recommended.

Mike, I don't know how much trouble it would cost to change my user name
wuxw or xiongwu. If it is not easy, I would be happy to keep xuxw.

Ross, thank you for committing my changes. Now Dave has added privileges
and I can commit without any trouble.


> -----Original Message-----
> From: David A. Case []
> Sent: Monday, April 18, 2005 9:51 PM
> To:
> Cc: Michael Crowley; Ross Walker
> Subject: Re: amber-developers: cvs amber9
> On Mon, Apr 18, 2005, Wu, Xiongwu (NIH/NHLBI) wrote:
> >
> > Sorry to bother you with my questions. Here I try to
> commit my changes in
> > file ips.f, ew_force.f, and force.f, but get a message says:
> > *** Access denied: Insufficient Karma (xuxw|amber9/src/sander)
> > cvs server: Pre-commit check failed
> I have added write permission for user "xuxw" (on
> to
> commit to Amber 9. I tried before as "wuxw", which doesn't
> match the password
> file on chagall.
> Is "xuxw" what you really want, or is it a typo by Mike? It
> seems less
> confusing to use your regular user name....
> Thanks for working on the parallel adaptation. Please look in
> amber9/test/gact_ips and in amber9/test/gb_rna to see if the
> new results are
> OK....they are different from wxwsander in Amber 8, but it
> looks like the same
> bug existed there as well. If the current results are OK, we
> should copy those
> into the "save" files.
> I have corrected another problem (I think): If you set ips=2
> (just IPS for
> electrostatics), then you should add in the continuum long-range vdw
> correction, but this was not being done. See revision 8.13
> of ew_force.f, and
> let me know if you see any problems. If I include this
> change, then I get
> essentially identical densities with PME or with IPS; without
> the change, the
> IPS=2 densities are too low by about 1% (which is what one
> would expect
> without the long-range vdw correction.)
> Thanks again for working on this!....dave
> --
> ==================================================================
> David A. Case | e-mail:
> 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 |
> ==================================================================
Received on Wed Apr 05 2006 - 23:49:58 PDT
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