AMBER Archive (2000)

Subject: parameters for GB use

From: Mark Forster (mforster_at_nibsc.ac.uk)
Date: Fri Nov 24 2000 - 03:58:51 CST

Dear Amber users

My question concerns the use of the Generalised Born (GB) solvation method.
Since the PME method is "always on" in the AMBER6 version of Sander
and PME is only intended for periodic system simulations,
how are the non bonded terms now computed in the case of the a GB
simulation in a non periodic system ?

Does the code then utilise atom based cutoffs and does the 'CUT' parameter
still control these terms ?

Finally, is the default value of SCEE=1.2 the correct value for a GB study ?

Thanks for any answers.

Mark 

--

  Dr Mark J Forster Ph.D.
  Principal Scientist
  Informatics Laboratory
  National Institute for Biological Standards and Control
  Blanche Lane, South Mimms,
  Hertfordshire EN6 3QG, United Kingdom.

  Tel  +44 (0)1707 654753
  FAX  +44 (0)1707 646730
  E-mail  mforster_at_nibsc.ac.uk