AMBER Archive (2002)

Subject: cut-off question

From: Cozmuta (ioana_at_wag.caltech.edu)
Date: Fri Sep 06 2002 - 17:49:21 CDT

Hi,

I did send the message below a couple of days ago but I did not get a
reply. So I am not sure if the question was to trivial or the message did
not reach the list (as I've changed my e-mail address from the one I show
up on the list).

Once again, I would appreciate any ideas.
Thanks,
Ioana

***********************
Date: Wed, 4 Sep 2002 12:43:38 -0700 (PDT)
From: Ioana Cozmuta <ioana_at_nas.nasa.gov>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: cut-off question

Hi amber users,

I have a question about the way to select the value of the
cutoff that you want to use in your calculations. Most of the literature I
read explains how to decide what cutoff to use in the case of PBC/minimum
image convention. What should be the correct way to decide what cutoff to
use when one does not use PBC? Would you start with a large cutoff (10%
larger than the maximum size of your system) and do single point energy
calculations for decreasing values of the cutoff. Then select the value of
the cutoff to use in the minimization/MD calculations for which the error
in calculating the energy is let's say smaller than 10% and also the
calculation time is reasonable? Any suggestions/ideas/references would be
welcomed.
Thanks, Ioana