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Pull request #2098 adds an infrastructure for adding unit tests for all kinds of force computing styles to LAMMPS. Currently only a handful of tests for a few representative pair styles have been ad…
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Hi TorchMD developers
I recently came across this repo and really liked it for its great software engineering. I will potentially use this for my own work. Hope you don't mind getting in touch.
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I'm writing a custom plugin to do a modified velocity-verlet integration with a new thermostat scheme. I wanted to optimize the number of force calculation so that it only calculate forces after posit…
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Is there a canonical way to test the energy conservation performance of our integrators? I'm finding reduced conservation as compared to Verlet, as measured by the below script.
```
import simtk.ope…
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The only issue I have with 404kph is : I felt so dumb browsing your repo !
I really enjoyed reading your code and I learned a ton !
I oscillated form amazement to stupefaction, jumped from head sc…
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Hi,
Thanks for the amazing software. I encountered an issue for energy conservation recently. I set a toy system, where I have two chains of beads, and beads in the same chain are connected with ne…
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@nilmeier, @swails, and I have been discussing ways we need to extend the OpenMM `app` layer's `ffxml` forcefield specification file format to be able to specify multiple protonation/tautomeric states…
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Execution of velocity verlet as well as leapfrog integration with 2D potentials leads to error: TypeError: can't multiply sequence by non-int of type 'float'. See example
`import os, sys
my_pat…
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http://www.deshawresearch.com/publications/Desmond-GPU%20Performance%20as%20of%20November%202016.pdf
I have not seen any comment on this, but the new Desmond finally showed good performance.
They…
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AMOEBA simulations still seem to have some subtle issues leading them to blow up with a fair amount of regularity. It pretty reliably happens every few hundred thousand steps. I suspect there is som…