Re: Using NBFIX

From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Tue Oct 31 2006 - 16:41:11 CST

I think there is a confusion between 'Sigma' and 'R_min' in LJ parameter.
NAMD use 'R_min' not 'Sigma'. For example, in my LJ parameter,

R_min = 5.27556 and
Sigma = R_min / 2^1/6 = 4.7.

Best,

-Hyon

sukesh shenoy wrote:
> I agree with Hyon when he says that NBFIX works. I see that as the r_min
> changes the radial distribution also changes. But i am not getting the
> expected results.
> I just want to clarify with hyon that when you enter the LJ parameters as
>
> P P -1.19503 5.27557 -0.00 0.00
> does this mean that at equilibrium the P P distance would be 5.27557
> Angstroms?
> Thanks,
> Sukesh
>
>
> */Hyonseok Hwang <danggi_at_northwestern.edu>/* wrote:
>
> 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*
> > > 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*
> >
> > >
> > >> 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
> > ****************************************
>
> --
> =======================================
> 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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-- 
=======================================
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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