I plan to use MD simulation to study a macromolecular system containing more than 300 million atoms after solvation. I am aware that large systems of up to a few million atoms have been successfully simulated at the atomistic level. But I haven't met many where up to 300 million particles have been studied. I will be grateful if you can recommend an MD code that can handle this. Thanks in anticipation.
I have simulated 200 million atoms about shock loading process with LAMMPS, it's an open source software.
The basic idea behind an MD simulation is straightforward. Given the positions of all the atoms in a biomolecular system (e.g., a protein surrounded by water and perhaps a lipid bilayer), one can calculate the force exerted on each atom by all the other atoms.
Dear Olujide Oludayo Olubiyi
For sure NAMD had been used alongside CHARMM force field to run large scale simulations of cromatophores
Article Molecular dynamics simulations of large macromolecular complexes
Article Light Harvesting by Lamellar Chromatophores in Rhodospirillu...
This was several year ago, so it's likely that large systems can now be handled by most of MD software. The point is having the computational facilities and the code correctly compiled to properly scale on the hardware you have
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