Re: amber-developers: extra points work

From: Robert Duke <>
Date: Thu, 22 Mar 2007 18:33:09 -0400

Hi Carlos -
I won't wait for the test cases - will keep going with getting stuff I can
test working for sure; I would just love to have a test case for the other
stuff prior to official release. Hopefully I will have something in less
than a week now; it has actually been a bit of a slog due to various
vagaries/complexities/needs to change infrastructure. When I do release it,
I will just mail a tarball to requestors (since the code has other work in
progress, and since I work on this stuff on my own, I tend to not check in
partial stuff).
Regards - Bob

----- Original Message -----
From: "Carlos Simmerling" <>
To: <>
Sent: Thursday, March 22, 2007 6:13 PM
Subject: Re: amber-developers: extra points work

> Bob,
> 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.
> thanks!
> Carlos
> 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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