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I think we're getting close to the point where we declare 7.0 feature complete and put out a beta. Are there any remaining features we want to wait for? I know of a few things that are in progress t…
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With the growing number of forcefields, the code including them needs to be restructured.
I prefer if the standard options are include in the script and give the possibility to read separate files by …
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In working toward making OpenMM more friendly toward small molecules and nonstandard residues, we've run into some nontrivial difficulties with the representation in `Topology` that relies only on con…
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Should our amber forcefields have Zinc? AFAIK these parameters are in the amber files, right?
```
kyleb@kyleb-DX4870:~/opt/pkgs/ambermini-14.0.1-0/dat/leap/parm$ cat parm99.dat |grep Zn
Zn 65.4 …
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@rafwiewiora is working on adding negatively charged versions of cysteine and histidine required for the multisite ion parameters (#1032). Since these new residue definitions do not appear in [`resid…
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We would like to refactor [`processAmberForceField.py`](https://github.com/pandegroup/openmm/blob/master/devtools/forcefield-scripts/processAmberForceField.py) to accomplish the following goals:
- Be …
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As Python threads always run in serial, it does not seem to be useful for performance to use threads in `FFLennardJones`. In fact, the `examples/pylj/paratemp` example runs about 3x faster on my machi…
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_From [watusim...@bitfighter.org](https://code.google.com/u/105427273526970468779/) on January 31, 2012 06:40:57_
When forcefields are detecting their endpoint (ForceFieldProjector::findForceFieldEnd…
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@ChayaSt and I are now working on conversion of AMBER and CHARMM parameters to ffxmls using ParmEd. Opening this for discussion.
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_From [buckyballreaction](https://code.google.com/u/buckyballreaction/) on February 03, 2011 17:28:35_
Robots will shoot down their own teams forcefields. TO replicate:
1. join the 'robots' server
2…