AMBER Archive (2001)

Subject: Re: TIP3P/SPC VdW radius

From: Jung-Hsing Lin (jlin_at_chemcca51.ucsd.edu)
Date: Tue Apr 10 2001 - 15:43:52 CDT

Hi! Artem,

I think your 1.5783 Ang is sigma, the vdW radius is 2^(1/6)*sigma.
So, 2^(1/6)*1.5783 = 1.7682 you will obtain the parameter given in AMBER
data base.

   CN1_ij CN2_ij sigma_ij 12 sigma_ij 6
  --------- - -------- = 4 epsilon_ij * ( (----------) + ( --------- ) )
    r_ij^12 r_ij^6 r_ij r_ij

  sigma_ij = sigma_i + sigma_j

R_ij* = 2^(1/6)*sigma_ij
  
   R_i* = 1/2 (R_ii)
  

I hope this helps,

Jung-Hsin

----------------------------------------------------------------------------
Jung-Hsin Lin, Dr. rer. nat.
Howard Hughes Medical Institute and
Department of Chemistry & Biochemistry TEL: +1 858 534 0956
University of California, San Diego FAX: +1 858 534 7042
9500 Gilman Drive, MC 0365 WWW: http://mccammon.ucsd.edu/~jlin/
La Jolla, CA 92093-0365 U.S.A.
----------------------------------------------------------------------------

On Tue, 10 Apr 2001, Thomas Huber wrote:

> Hi Artem,
>
> if you compare different papers about vdW radii, then you have to look for
> the particular definition of the radius. Sometimes they are defined as the
> half of the distance between identical atoms at minimum interaction
> energy, and as I recall (unfortunately I don't have the time to look it
> up) as the half of the distance at zero (!) interaction energy, which
> would correspond to the hard spere radius.
> Regardless of the actual definition, each paper should describe the
> analytical term to calculate the interaction energy, so if you have a
> parameter set and an equation, just fill in the values into the formula
> and compare it with the other paper. After some rearrangements, you'll
> probably find the parameters of being equivalent.
>
> Thomas
>
> -----------------------------------------------------------------------------
> Dr.Thomas Huber University of Arizona
> Tel.: (520) 621-2537 Department of Chemistry
> FAX: (520) 621-8407 1306 E. University Blvd.
> email thuber_at_physik.tu-muenchen.de Tucson, Arizona 85721-0041
>
> On Tue, 10 Apr 2001, artem wrote:
>
> > Dear Amber users,
> >
> > I've noticed that Van der Waals radius for TIP3P in Amber (parm94.dat)
> > is different from original TIP3P model reported in J. Chem. Phys., 1983,
> > 79, 926-935. Amber has 1.7683 angs and the original has 1.5753 angs. I
> > can assume that Amber's radius comes from some additional
> > parametrisation. Does anybody have references about the justificationof
> > Amber's TIP3P Van der Waals radius? What radius should i use if i wantto
> > switch on SPC model?
> >
> > thanks a lot
> >
> > Artem Mamonov
> > Chemistry Department
> > University of Pittsburgh
> >
> >
>
>