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How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here: The main issue are the units. The input parameters for reax force fields ...
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Does increasing Lennard-Jones cutoff means higher accuracy?

I am afraid I can't be of much help regarding the QM part of your simulation, but I can give some thoughts on the MM part. In short: you should use the cutoff that was used to validate your force ...
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• 1,294
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Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

You may be able to find some bounds on performance such as O(n3) based on the number of water molecules etc, but honestly benchmarks not performed on your own hardware are always somewhat hard to use ...
• 10.1k
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What are the more efficient, or easier, methods of handling electromagnetic interactions?

You could simplify long range interaction by reducing precision with range. Useful algorithm for it is: https://en.wikipedia.org/wiki/Barnes%E2%80%93Hut_simulation It is usually used for gravity, but ...