Re: amber-developers: extra points work

From: Carlos Simmerling <>
Date: Thu, 22 Mar 2007 18:13:39 -0400

that's great news. I don't have any EP test cases, but it would be wonderful
if you could push out the TIP4P support ASAP as we're burning through
time right now doing it in sander. I think we'd all rather not wait
until full EP
support is in and debugged.

On 3/22/07, Robert Duke <> wrote:
> Folks -
> Okay, I have parallelization issues yet, as well as fixes needed to zero the
> extra points velocities (these are bogus in sander currently, though it is
> the sort of thing people don't care about until they start comparing
> outputs - it basically does not matter except for program consistency, as
> the velocity on an ep is not used...). However, I basically have tip4p and
> tip5p working. Now, it would be great if I had some more complex test cases.
> The ubiquitin and dna_pol test cases both require ipol=1, which I don't
> intend to support. Does anyone have any other model systems that use extra
> points (preferably something that will test the more complex frame types)
> but don't require ipol == 1?
> Thanks - Bob

Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology   Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University        E-mail:
Stony Brook, NY 11794-5115
Received on Sun Mar 25 2007 - 06:07:31 PDT
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