Re: Using NBFIX

From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Sun Oct 29 2006 - 20:44:30 CST

Hi,
I'm wondering why it didn't work for you.
At that moment, I didn't notice, but maybe it could be important to
leave the NONBONDED part in the parameter file even if you don't use it.

For example, I have NONBONDED part in the paramter file:

NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
! ignore Emin Rmin/2 ignore Emin1,4 Rmin/2,1,4
P 0.0 -0.000 0.00 0.00 -0.000 0.00
N0 0.0 -0.000 0.00 0.00 -0.000 0.00
ND 0.0 -0.000 0.00 0.00 -0.000 0.00

And after that part, I have the NBFIX:
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'm not so sure if this is the problem you have. You may try.
Thanks.

-Hyon

Neelanjana Sengupta wrote:
> Hi,
> I had tried this some months back, and this is the format I used
> (suggested by Hyonsek). However, it did not seem to work for me... I did
> not notice the changes I was expecting. If you find that it works,
> PLEASE let me know! Below is my correspondence with Hyonsek:
> ------------------------
> 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
>
>
> On 10/28/06, * sukesh shenoy* <sukesh_shenoy_at_yahoo.co.in
> <mailto:sukesh_shenoy_at_yahoo.co.in>> wrote:
>
> I am trying to use NBFIX to incorporate lenard jones parameters for
> a CN bond with E_min = 61.9 Kcal/mol and equilibrium C-N length =
> 1.5 A. Can anyone please tell me how to put these parameters in the
> correct format for NBFIX.
>
> Sukesh
>
> ------------------------------------------------------------------------
>
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> USA
> Phone: 1-949-824 9921
> email: sengupta_at_uci.edu <mailto:sengupta_at_uci.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
=======================================

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:51 CST