From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Mon Oct 30 2006 - 01:05:03 CST
Yes, it definitely works for me. As you can see, the LJ parameters of
the NONBONDED part in my parameter file are all zero's, so if my
simulation takes the LJ parameters from the NONBONDED part, it doesn't
run correctly. So I'm sure that my simulation takes the parameters from
the NBFIX part and runs well.
Please take a look at the LJ energy term in the log file with and
without the NBFIX part and check if the LJ energy term is changing or
not, then you can see if the LJ parameters in NBFIX part are taken or not.
Best,
-Hyon
Neelanjana Sengupta wrote:
> 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
> <mailto: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>
> > <mailto: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 <mailto: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 <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 =======================================
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