From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Nov 06 2003 - 14:10:49 CST
Hello Elena
First suggestion, try the final 2.5 version of NAMD, if nothing else it
will clean up the log file.
Second, and I hope Jim or somone else will correct me if I am wrong, but
the protein-rattle algorithm can't handle a single energy pulse of 313K.
I have received similar warnings when first using namd without first
trying to
heat the protein/water system gradually.
Brian
On Thu, 6 Nov 2003, ELENA JEAN LEVIN wrote:
> Hi,
>
> I'm a new NAMD user trying to run a simple
> minimization and equilibration of a kinase in a
> water box, using the online tutorial as a guide as
> well as the help of another student who has
> attended the summer workshop at IUIC. We first ran
> the simulation with the protein fixed and only the
> water molecules moving, and did not encounter any
> problems. However, when we then tried continuing
> with both the protein and water molecules unfixed,
> we kept getting a "constraint failure in RATTLE
> algorithm" error message for the same ten atoms
> each time. We've tried the two suggestions given
> in the namd-l archive to someone experiencing a
> similar problem, increasing the boundary sizes and
> increasing the number of minimization steps, but
> to no effect. We had the same problem with the
> ubiquitin tutorial, even though the grad student
> I'm working with swears he's following the exact
> same steps as at the UIUC workshop. Does anyone
> have an idea as to what could be going wrong?
> We've put the log, configuration and other files
> that we're using online:
>
> <a
> href="http://www.sit.wisc.edu/~rmbannen/namd/waku.conf">configuration
> file</a>
> <a
> href="http://www.sit.wisc.edu/~rmbannen/namd/waku.log">log
> file</a>
> <a
> href="http://www.sit.wisc.edu/~rmbannen/namd/wak.psf">Solvated
> AK psf</a>
> <a
> href="http://www.sit.wisc.edu/~rmbannen/namd/wak_out4.pdb">Solvated
> AK pdb</a>
>
>
> Thanks,
>
> Elena Levin
>
> Department of Biochemistry
> University of Wisconsin, Madison
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** *****************************************************************
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