On Fri, Nov 14, 2003, raist.mmb.pcb.ub.es wrote:
> I'm running a MD on a 8-MER DNA using amber7. I restart the simulation
> with coordinates and velocities from the previous run every 200ps. On one
> of this restartings the MD died because of a large deviation between two
> atoms(common SHAKE error)
The imaging one would do in ptraj is only for visualization; it should have
nothing to do with SHAKE. In any event, you would not have a SHAKE constraint
between two strands (I would imagine).
I have no idea why what you did had an effect. You didn't say how soon after
the restart the SHAKE failure occurred in the run that failed. Did it happen
on the very first step, or later on? SHAKE failures during runs are chaotic
events, so *any* change in starting coordinates could lead to a new trajectory
that might not exhibit the problem. This could be an explanation for the
behavior you see.
Try a larger value of taup (the default is really too small). Try setting
ntc=ntf=2, not 3. If neither of those helps, you may need to use a shorter
time step.
...good luck...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 Fri Nov 14 2003 - 16:53:01 PST
