Scattering function F(q)

Calculating S(q)...

It seems that in the new version of gromacs only the option to calculate SANS spectra has survived... If it is not so please tell me!!!! If, unfortunatelly, I am right I explain shortly how toclculate a f(q). I have even created a small FORTRAN code to do that.

Basically the program calculates the total G(r) weighted by the Neutron Scattering Cross Section, and then performs a Fourier transofrmation.

Firs of all you have to create the index files. To do that have a look at your confout.gro and keep in mind the names of the atoms. Then write

  • gmx make_ndx -f confout.gro

And let the party begin. First of all we create a series of indexes with the name of the atoms writing something like:

  • a C*
  • a H*
  • a N*
  • a O*

This will generate indexes for Carbon, Hydrogen, Nitrogen and Oxygen... the star, as usually, means "starting with". So if you want to select one kind of atoms (for example CT3) you have to write a CT3... You must now write down the numbers (you can also rename the groups so that instead of having a number they have a name with something like  "name 3 N", that will rename the group 3 to Nitrogen. You can now write "q" to save and quit.

Now we will calculate the g(r) for all combinations. To do that I wrote a small fortran code that can be downloaded from this SQ dropbox folder.

The program will calculate all possible g(r) reading the traj.trr file, will sum up all of them and will perform a Furier transformation.... if you are lucky.