Assuming I want to use Gromacs, what do I need to pull a molecule thorugh a protein. The molecule is already in there, I just need to see if it can freely go from one part to another. I can write a script in python to do it, but I don't know if there is a general procedure or not. A good article about this would help a lot. Is it enough to start pulling an atom? Or all of them? Do I need to pull the protein the other way? Or should I fix the molecule to stay within a box?
Any help is appreciated :D
https://kbbox.h-its.org/toolbox/methods/molecular-simulation/-random-acceleration-molecular-dynamics-ramd/
https://manual.gromacs.org/2024.0/reference-manual/special/pulling.html
To pull a molecule through a protein in GROMACS, you typically use steered molecular dynamics (SMD). You can apply a harmonic potential to a specific atom of the molecule or the center of mass to move it. It's usually best to pull only the molecule and not the protein unless studying protein deformation. Fixing the molecule in the simulation box isn’t necessary unless you want to restrict its movement. For a detailed guide, check GROMACS documentation on "Steered MD" or related articles.
o pull a molecule through a protein in GROMACS:
Check relevant GROMACS documentation or articles on "Pulling simulations" for detailed guidance.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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