[gmx-users] dummy constant calculations

[David van der Spoel]

On Fri, 2004-11-12 at 17:00 +0200, Arturas wrote:
> I am stucked on the calculations of a, c and c constants for dummies
> in 'tip5p.itp' file. I could not get the same or very similar values
> as the numbers in the file. However, theres is still unclear points.
> 
> 
> a=b= 0.07 * cos(109.47/2) / | xOH1 + xOH2 |, where | xOH1 + xOH2 | =
> = 2 | xOH1 | cos (H1-O-H2).
> 
> I assume that:
> 2 | xOH1 | cos (H1-O-H2) == 2 * xOH1 * cos(H1-O-H2)         ????
> H1-O-H2 = 109.47, because there is a tetrahedral system.    ????
> xOH1 & xOH2 = 0.1 nm , i.e. approximate O-H bond distance.  ????
> 
> Maybe I am interpret the math expression wrong ?
I don't recall, but it looks correct. You can simply try it and measure
distances with rasmol or so afterwards.
> 
> 
> Arturas
> 
> 
> 
> 
> 
> 
> |----->
> >> I checked 'tip5p.itp' file for how dummies were constructed.
> >> Where I could find explanation how constants a, b , etc. are
> >> calculated for topology ?
> >> 
> >> There are entries like  | xOH1 + xOH2 | and so on. xOH1 - does it
> >> correspond to the O-H bond length ?
> DvdS> Yes, but do check the manual as well...
> <-----|
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++