On Tue, Jul 15, 2003, Anton B. Guliaev wrote:
>
> I am facing an old problem with MD -- each time I tried to restart my
> simulation after minimization or initial structure the system crashes with
> the message:
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 8 87 243 244
Are you routinely running a 10-step minimization (without shake), printing the
energy every step? Are the vdW (and other) energies reasonable? Same
question with 100 step minimization. Does the potential energy at the first
step of MD match the last step you got from minimization?
These are the sorts of questions you should be asking. It's often good to
use the "checkoverlap" command of ptraj to find problems (esp. with a periodic
simulation) for models that may still "look pretty decent", as you report.
...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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 16 2003 - 02:53:01 PDT
