From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Oct 30 2006 - 00:17:50 CST
Hi Hyon,
Thanks for the update... I'll try this whenever I am free. Do you remember
if it worked for you (ie. you got things that were expected)?
I was trying to implement some solvent models in NAMD, which had explicit
cross terms. I was checking things like the radial distribution functions
from my simulations---- I did not notice any changes with and without NBFIX.
(And rad. disb. fn. has sensitve dependencies at least on the r_min term).
Regards,
Neelanjana
On 10/29/06, Hyonseok Hwang <danggi_at_northwestern.edu> wrote:
>
> 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
> >
> >
> ------------------------------------------------------------------------
> --
> =======================================
> 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
> =======================================
>
>
-- **************************************** 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 ****************************************
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