Robert Matthew Fesinmeyer writes:
>I wrote a while back asking about some problems I had with SANDER runs
>ending with:
>
> COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
> WITHIN 3000 ITERATIONS
>
I've only noticed this problem when I had situations that SHAKE
couldn't get itself out of, for example, where it would cause some
sort of very close atom contact or other energetically unfavorable
configuration. I usually had to modify my protocol during the
equilibration phase, such that the water and solute were in more favorable
contact, and the solute was properly "relaxed" (IE energy minimized)
in vacuo before commencing production runs at 300K.
Does the problem happen when you use dt=0.001?
Dave
Received on Mon Jun 26 2000 - 15:55:05 PDT
