I want the density profile of a solvent in a particular direction when we have the trajectory file from molecular dynamics simulation. For example, analyzing the solvent density around a protein of interest or a graphene sheet. I have attached a similar analysis from a paper where you can see the density profiles below the trajectories.
Thank you!
Use TRAVIS. Is by far the best MD analysis tool, and it is free
http://www.travis-analyzer.de
If you are into Python, you could use the library Biotite (https://www.biotite-python.org/) I am developing. You would load the structure, filter the solvent molecule and create a histogram of the x, y or z coordinates using NumPy. If tyou require another axis you could rotate the atoms to one of these axes with biotite.structure.align_vectors().
If this is still relevant for you, I offer to write a small dummy script for this purpose.
Another python package that may do the job is MDAnalysis:
https://docs.mdanalysis.org/stable/documentation_pages/analysis/density.html
'4.8.1.1. Generating a density from a MD trajectory
A common use case is to analyze the solvent density around a protein of interest.'
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