I have performed MD simulations on a particular system, this is a molecular system in water. Upon simulating I can see that the molecules gain some form of order. I would like to know if it is possible to derive and plot a calculated XRD pattern or calculated 2D Scattering Factor patterns from a structure file only ( say .pdb or .mol2 ) with no header information?
There are roughly 800 molecules in the simulation, these molecules have "frozen" and are now potentially crystalline, I would like to derive the 2D structure factor or calculated 2D Single Crystal XRD pattern (or both!) for this. Unfortunately the output from a GROMACS simulation can be in .pdb or .gro or .mol2 format at best and I cannot understand how I can calculate and plot the aforementioned quantities.
Any and all help is greatly appreciated! It would be better to know tools which are Open Source as well.
Dear Rituparno Chowdhury ,
In principle, to simulate 2D or 3D XRD patterns, it is necessary the cell descriptors, in general the crystal structure itself descriptors.
The pdb file has the necessary information, mol2 in general speaking has no enough information to generate the XRD pattern.
The free FullProf suite can be used by not enabling the fitting in the command line, only the plot of the crystal structure. The generated structure may be visualised using the internal program FullProf Studio, developed for visualisation of crystal and magnetic structures. Otherwise, there is a public domain program VESTA, that enable pdb file importing.
In the FullProf Suite, you may use single crystal data or integrated intensities (alone or in combination with a powder profile).
Neutron (or X-ray) powder patterns can be mixed with integrated intensities of X-ray (or neutron) for single crystal or powder data.
I am not sure the single-crystal readings' simulation is still enabled.
Need to explore.
I hope it helps somehow.
Best regards,
WNM
Ok I see, I will try to use the FullProf Suite and get back to you.
Thank you so much!
If you have a bunch of atomic positions from your simulation, then you need to use the debye formula. Maybe a program like Debyer.
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