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This issue is for discussing how we should generate solvated input files for various codes.
Questions:
- Which codes should we support?
- What is our goal? To make sure the systems are as identical …
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Just wanted to document and discuss the routes for openff-interchange replacing the functionality of InterMol. Note that there is no guarantee that all of these things will supported at any particular…
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YANK currently prints out a ton of output, almost none of which is relevant for most users.
We should figure out what information needs to be printed out and just print that.
Even better would be to…
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I am wondering if the attention score calculation could be vectorized to run per batch instead of running two loops (batch size x encoder time steps)
The sections of code are here:
```
class Attn…
pravn updated
6 years ago
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## Motivation
Membrane-protein systems account for ~ 60% of possible target space. Being able to calculate binding free energies for membrane-containing systems would be a significant advantage.
…
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### Description of the enhancement or error report
We need to add .md documentation for the grand potential model. This needs to include a page on derivations and a page with examples how to use this…
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I'm getting different solvation energies for water by using the xtb commandline interface and python interface.
Input:
```
3 …
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I am running some tests on my system and I am getting quite high energies as for free energy of binding (~200 kcal/mol). In my current setup I am using `resid x to y` to select the ligand. Even thoug…
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There are various free energy methods that utilize scaling of intermolecular interactions. For example one can compute the chemical potential by inserting an additional particle/molecule into the syst…
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1) specify available units and type of notation (i.e. kcal/mol vs kcal.mol-1 and kJ/mol or eV or..)
2) Everything seems crystal clear except the meaning of "(When the --relative flag is specified i…