On Fri, Nov 15, 2002, Tod Pascal wrote:
> I was going through the tutorial on the website, attempting to simulate
> a holiday junction. After I solvate the molecule and add the
> counter-ions, I attempt to run a short minimization run to remove any
> potentially bad contacts (as described under the DNA tutorial as Step
> one). This work, however for the next step (Dynamics holding the solute
> fixed), it crashes and give me this error:
>
> vlimit exceeded for step 0; vmax = 60.1534683
>
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 1 27 28
>
> I'm following the tutorial as written, only using the holiday junction
> pdb file. What am I doing wrong?
>
looks like you still have bad initial forces; start with tempi=0 (if you
didn't do that already). If that still fails, you will probably have to
do more minimization before starting dynamics.
..good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_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
==================================================================
Received on Mon Nov 18 2002 - 16:29:22 PST
