Hi David,
I reduced the time step to 0.001 AND I tried slowly heating, AND increased
taup value. There is def a non-standard molecue in the forcefield. its a
porphyrin derivative.
Hey Bill, Im going to try that idea next! Thx. Ill get back with you guys
once I run it. :) Happy Tuesday, Justine
On Tue, Oct 12, 2010 at 2:15 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Oct 12, 2010, Justine Shaw wrote:
>
> > Now I am getting seg fault errors running with no shake and an NTP
> > simulation!?
>
> If you have waters, you *must* use shake. If you see SHAKE errors, try
> reducing the time step (to 0.001 or even lower at the beginning), and
> arrange
> to heat more slowly, and change the volume more slowly (i.e. a larger value
> of
> taup.) If you have non-standard items in the force field, there may be
> some
> instability there...I've lost track a bit of this thread. Some failures
> can
> be tough to track down, but a "shake failure" is almost never cured by
> turning
> shake off.
>
> ...good luck....dac
>
>
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--
*****************************
Justine A. Shaw -PhD Candidate
ΦΛΥ '09-'10 Service Chair
Profs. Ratner and Meade Research Groups
Department of Chemistry
Northwestern University
Office: 4039 Nano (Ryan Hall)
Office Phone: 847 467 4991
Cell: 773-354-7135
Email: j-shaw.northwestern.edu
*************************************
"Let's do this....!"
-Justine Shaw
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Received on Tue Oct 12 2010 - 15:00:04 PDT
