On Sun, Nov 16, 2003, Yong Duan wrote:
>
> Although the first step energies of sander and pmemd agree to the last
> digit, after a while (within 10ps) the energies of the two may start to
> show difference withi a notable change in the energies by pmemd. The
> pmemd energies stabilize at a new level which is not too different from
> the one by sander, but nevertheless noticeable (about the level of
> fluctuation). Has anybody else noticed it?
Just make sure that this is not something simple, like not have the
correct
value for amber7_compat set in the pmemd run. And, what is the difference
in the mean energies? Is there constant temperature or constant pressure
turned on?
>
> Secondly, for some reason, I keep getting "FLUSH--FAILED:: Resource
> temporarily unavailable" from sander on Xeon/mpich/ifc/static
> combination.
>
We get this too, but I don't know where it is coming from. We will
probably
have to special-case how the mdinfo file is handled for this architecture.
.dac
--
==================================================================
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
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Received on Wed Apr 05 2006 - 23:50:06 PDT
