Arthur Roberts wrote:
Hi, All,
I would like to thank Carsten Kutzner, Erik Lindahl,
and David van der Spoel for their advise with my
previous problem with not getting any data with mdrun.
It turned out to be due to the fourier spacing and
the PME order. In addition, David van der Spoel's
suggestion of using a water shell was quite useful for
troubleshooting.
I have a new problem:
When pressure coupling is used with mdrun, I get the
following error:
Step 209 Warning: pressure scaling more than 1%, mu:
1.02233 1.02233 1.02233
I tried lengthening the tau_p to 4, but it didn't help
as recommended for a similar problem in the mail
archives.
is the system well minimized and equilibrated?
you can try running without pressure coupling for a while.
then you can try running without PME for testing only..
Details of the problem can be found here:
http://cetus.mchem.washington.edu/pub/supercomputer/Pressure%20causes%20errors.html
Best wishes,
Art
University of Washington
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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