Dear AMBER users,
I am performing MD simulation on a solvated DNA
with some constraints on one of the bases (sander in amber6).
Sometimes SHAKE fails after hundreds of ps of
simulation with:
COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
DEVIATION IS TOO LARGE
NITER, NIT, LL, I AND J ARE : 0 1 216 633 634
It seems that the shake iteration doesn't even start
as the bond parameter tolerance is exceeded.
Now, I don't really want to abandon shake and the 2 fs
timestep.
Can I and should I persuade shake to reset this coordinate
or would it be possible to leave out this bond (or the solute bonds)
from shake?
Any suggestion would be welcome!
Thanks for your help.
Peter Varnai
Received on Thu Aug 30 2001 - 06:57:00 PDT
