[gmx-users] g_density for a micelle

[Tsjerk Wassenaar]

Hi Chris,

Have a look at Makefile.am in the directory src/tools/ You can add
g(mx)_rdf_mod whereever you find g_rdf, following the logic of the
format. Then run automake (make sure it's the right version) and run
./configure from the gromacs directory. Finally, in src/tools/ issuing
make g_rdf_mod should then work.

Best,

Tsjerk

On 11/12/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
>
> > Hi Chris,
> >
> > Aren't you looking for a radial distribution function (g_rdf)? Maybe
> > you'll have to change the code a bit to get exactly what you want, but
> > I'd guess that g_rdf is closer to what you want. However, you do not
> > state what it is you want.., so it's merely a guess.
> >
> > Best,
> >
>
> Of course you are correct, thanks. What I want is a histogram of the
> distance from the center of mass of the micelle for each heavy atom
> individually.
>
> I have used g_rdf -com as suggested by Tsjerk. I then wrote a g_vol.c
> program that used a loop over:
>
> do{
>    vol = det(fr.box);
>    sumvol+=vol;
>    numfr++;
> } while(read_next_frame(status,&fr));
> vol=sumvol/(double)numfr;
>
> Multiplying each rdf value by the shell volume {4/3*pi*(r^3-(r-dr)^3)}
> and dividing by the total volume from g_vol gives a probability
> histogram that is already normalized for the number of molecules in
> the micelle.
>
> This gives the correct answer for constant volume simulations and very
> nearly the correct answer for constant pressure simulations (close
> enough that I am satisfied with it). I could directly modify g_rdf,
> but I have had trouble compiling seperate tools other than those that
> I build myself based on template.c. How would one compile g_rdf only
> after modifying the source code? Preferably, how would one copy
> g_rdf/gmx_rdf to g_rdf_mod/gmx_rdf_mod and compile them?
>
> Thanks again,
> Chris.
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623