From: Stern, Julie (jvstern_at_bnl.gov)
Date: Thu May 12 2005 - 11:47:01 CDT
Hi,
The scnb scaling factor I was using was 1.0 and the default is 2.0. The
1-4 vdw interactions get divided by scnb. I was now told that the amber
force fields are fit to default values for these scaling factors and if we
don't use the default value we can't say we are using amber force fields.
It says in the NAMD manual that scnb should be set to the inverse of the
default
of scee (the 1-4 electrostatic interaction scaling which multiplies it which
in NAMD is 1-4scaling) in AMBER which is 1.2. Hence, that means 1-4scaling
should be defaulted to the inverse of 1.2 which is .83. The default for
1-4scaling
is 1.0 and that's also what I had.
An AMBER developer was surprised we were even allowed to set these values as
users.
So, what do you think the impact on my results are for running with 1.0
for
both scnb and the 1-4scaling from the physical point of view, when the
default
for scnb is 2.0 and 1-4scaling should apparently be .83?
Where in the force field exactly is this affected?
Thanks.
--Julie
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