From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 10 2012 - 08:02:18 CDT
On Mon, Sep 10, 2012 at 2:56 PM, Marc Gordon <marcgrdn55_at_gmail.com> wrote:
> 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.
for AMBER inputs.
[...]
> 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)
because that is what amber uses most commonly.
(1-4 LJ scaled by 0.5 and 1-4 coulomb scaled by 5/6th)
axel.
>
>
> 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.
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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