Re: scnb value to prevent VDWs scaling

From: Marc Gordon (marcgrdn55_at_gmail.com)
Date: Mon Sep 10 2012 - 07:56:44 CDT

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 that the
vdws interactions are divided by the scnb values.

It follows with common sense that a value of 1 would result in no scaling
if dividing is happening. Perhaps further support for this is that the
minimum value is 1, but I didn't want to just assume that and was wondering
if someone had asked that question before and perhaps had an answer.

Anyway the more I think about the more I think common sense has a point
here and that you guys are right.

Thanks guys.

On a related note then do you guys happen to have any idea as to why NAMD
would scale vdw interactions to half by default? (default value of scnb is
2)

Marc

On Sat, Sep 8, 2012 at 1:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Sep 8, 2012 at 12:21 PM, Marc Gordon <marcgrdn55_at_gmail.com> wrote:
> > HI Norman
> >
> > Yes that is what I thought but I couldn't find it explicitly confirmed in
>
> actually it is *not* quite that.
>
> > the NAMD documentation and didn't want to just assume I had it right.
>
> but it *is* described in the NAMD documentation. here is the first hit
> to show when one uses the "search user's guide" dialog.
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html
>
> cheers,
> axel.
>
> >
> >
> > Regards
> > Marc
> >
> >
> > On Thu, Sep 6, 2012 at 3:09 PM, Norman Geist
> > <norman.geist_at_uni-greifswald.de> wrote:
> >>
> >> scnb = „scale non bonded“
> >>
> >>
> >>
> >> so common sense would say that a factor of 1 will not change anything to
> >> the incoming ff.
> >>
> >>
> >>
> >> Norman Geist.
> >>
> >>
> >>
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag
> >> von Marc Gordon
> >> Gesendet: Donnerstag, 6. September 2012 14:27
> >> An: namd-l_at_ks.uiuc.edu
> >> Betreff: Re: namd-l: scnb value to prevent VDWs scaling
> >>
> >>
> >>
> >> Hi all
> >>
> >>
> >>
> >> Didn't get a response to this and I really need an answer so I thought I
> >> should bump it.
> >>
> >> Please if anyone has an answer for me it would be much appreciated.
> >>
> >>
> >> Regards
> >> Marc
> >>
> >> On Mon, Aug 13, 2012 at 3:40 PM, Marc Gordon <marcgrdn55_at_gmail.com>
> wrote:
> >>
> >> Hi all
> >>
> >> I'm trying to find out what scnb figure in NAMD results in no scaling. I
> >> gather from the user guide that the default is 2 and that the VDWs
> >> interactions are divided by the scnb value.
> >>
> >> It seems to me that an scnb value of 1 would then be required to achieve
> >> no scaling (or a scaling factor of 1 anyway) of VDWs interactions. Just
> >> thought I would check. Am I correct in this?
> >>
> >>
> >> Regards
> >> Marc
> >>
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:03 CST