From: Marc Gordon (marcgrdn55_at_gmail.com)
Date: Mon Sep 10 2012 - 08:45:24 CDT
Wow I didn't get that from the NAMD documentation at all but it makes
sense. This clears up a lot of confusion for me.
Thank you Axel this has been very helpful.
On Mon, Sep 10, 2012 at 3:33 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Sep 10, 2012 at 3:28 PM, Marc Gordon <marcgrdn55_at_gmail.com> wrote:
> > Hi Axel thanks for the prompt response.
> > On Mon, Sep 10, 2012 at 3:02 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> On Mon, Sep 10, 2012 at 2:56 PM, Marc Gordon <marcgrdn55_at_gmail.com>
> >> > Hi Axel
> >> >
> >> > The NAMD documentation for sure mentions scnb but as I said it doesn't
> >> > explicitly say that an scnb value of 1 results in no scaling. Just
> >> the
> >> > vdws interactions are divided by the scnb values.
> >> for AMBER inputs.
> >> [...]
> > Wait... for AMBER inputs?
> > So scnb is not even considered unless the 'amber' option is set to 'yes'?
> > .. so it is defaulted to 1 with charmm inputs?
> yes. 1-4 LJ interactions for CHARMM are not scaled.
> there are a limited number of atom types that have
> modified epsilon and sigma for 14 interactions.
> those are explicitly listed in the CHARMM parameter file.
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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