Calculate SDF(Spatial distribution function)

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Dhia Adnan Hanoush

I Think u could try the open source software, Large-scale Atomic/Molecular Massively Parallel Simulator

(LAMMPS)

Lee Clawson

I don't have a specific program in mind. But I can offer these links to possible ideas for a better solution....

1)__ Distrubutions of Counterions around DNA.

Molecular Dynamics Simulations Results

We have carried out a series of molecular dynamics simulations of DNA (see details below) in presence of water and three types of counterions: Li, Na and Cs. The results on spatial distributions of ions, diffusion of ions near the DNA surface and on effective (solvent-mediated) ion-DNA interaction potentials will be published soon. See Link below...

http://www.fos.su.se/~sasha/mdynamix/Examples/dna_sim/

2__ Spatial distribution functions: sdf.f

This utility computes spatial distribution functions and creates a file which can be visualized using gOpenMol package (http://.www.csc.fi/gopenmol/).

See this link....

http://www.fos.su.se/~sasha/mdynamix/MDX_manual/node45.html

3)__ GMX Spatial

GMX Spatial calculates the spatial distribution function and outputs it in a form that can be read by VMD as Gaussian98 cube format.

https://manual.gromacs.org/archive/5.0.7/programs/gmx-spatial.html

4)__ Application of the Spatial Distribution Function to Colloidal Ordering

https://pubs.acs.org/doi/10.1021/acs.langmuir.9b02877

5)__ Search Results Using Google Scholar for:

"Calculate Spatial distribution function"

(...An alternative to normal search...)

See this link for a listing of scholarly articles and papers

https://scholar.google.com/scholar?q=Calculate+Spatial+distribution+function&hl=en&as_sdt=0&as_vis=1&oi=scholart

Andresa Messias da Silva

Lee Clawson thank you so much!