From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Tue Jul 25 2006 - 21:33:14 CDT
I'm pretty sure that is Rmin not Rmin/2. Actually, Rmin/2 is meaningless
in that situation.
And I guess that the other two parameters are related to 1-4
interactions, but I'm not sure.
If I remember correctly, I found the information on the 'NBFIX' from the
NAMD version 1.5 user's guide. If you are googling, I think you can find
the NAMD 1.5 user's guide on the web.
Best,
-Hyon
Neelanjana Sengupta wrote:
> Thanks!
> Just to be sure, the second parameter is 'Rmin' and not 'Rmin/2' ? Also,
> do you know what the other two parameters are?
> Regards,
> Neela
>
> On 7/25/06, * Hyonseok Hwang* <danggi_at_northwestern.edu
> <mailto:danggi_at_northwestern.edu>> wrote:
>
> Yes, you can do it in the 2.6b1.
> Below is how I'm using it in my parameter input file.
>
> NBFIX
> !
> !type1 type2 Emin Rmin
> ! (Kcal/mol) (A)
> !
>
> P P - 1.19503 5.27557 -0.00 0.00
> P N0 -0.62142 5.27557 -0.00 0.00
> P ND -0.81262 5.27557 -0.00 0.00
>
>
> I hope this will be of some help.
>
> Best,
>
> -Hyon
>
>
> Neelanjana Sengupta wrote:
> > Hi,
> > I apologize for asking a redundant question, but I did not find any
> > definite answers in the mail archive.
> > Can NBFix be used in the latest version ( 2.6b1) of NAMD? Or, is
> there a
> > way of including cross-terms in the Lennard Jones parameters, in the
> > CHARMM format parameter files?
> > (Specifically, I am trying to set up parameters for Chloroform,
> and the
> > model I'm trying to use includes non-bonded interactions between the
> > different atoms types).
> >
> > Thanks,
> > Neela
>
> --
> =======================================
> Hyonseok Hwang
> Postdoctoral Fellow
> Department of Chemistry
> Northwestern University
> 2145 Sheridan Rd.
> Evanston, IL 60208-3113 USA
> ---------------------------------------
> Tel:(847)467-4987(O)
> Email:danggi_at_northwestern.edu <mailto:Email:danggi_at_northwestern.edu>
> =======================================
>
>
-- ======================================= Hyonseok Hwang Postdoctoral Fellow Department of Chemistry Northwestern University 2145 Sheridan Rd. Evanston, IL 60208-3113 USA --------------------------------------- Tel:(847)467-4987(O) Email:danggi_at_northwestern.edu =======================================
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