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This issue is a container for requests related to additions of new parser entries.
- additional energy entries
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So analyze.py has lots of trajectory analysis code that duplicates things I've already written in MDTraj. We can replace a lot of this redundant code with only a few lines of MDTraj code.
There is…
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Brainstorming things to do before we can start using this code more reliably.
Tagging @jchodera @gregoryross, feel free to add points by editing (assuming you can) or replying.
- [x] Clean up the r…
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While spot-checking some gas-phase simulations of molecules from FreeSolv parameterized using SMIRNOFF, one molecule that caught our eye in particular was "aldicarb" (ID within FreeSolv: 'mobley_52003…
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Hi
I created a branch vsites2 and uploaded the changes contained in one commit here:
https://github.com/bieniekmateusz/Sire/tree/vsites2
There are some useful code snippets I left in the code t…
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Yesterday I defended my master's thesis, and my supervisor has approved my thesis as complete. The XPS spectrum was analyzed with LG4X and plotted with Matplotlib after I exported the data.
The sad…
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Dear all,
I am trying to create a pipeline to automate the binding energy calculation of several variants of a homotetrameric protein in complex with a medium/big-sized ligand (CoA). I haven't deci…
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Dear Psi4 Developers,
Could you add an option for doing finite temperature DFT?
I find that there already exists an option for allowing fractional occupation number (FON) to accelerate SCF, so i…
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I followed instruction to install singularity 3.8.2 and Go,
During starting, the errors happened as below.
==============================================
Generating the working folder...
Running …
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WaterSwap seems to be broken in the current development version of Flare and it also throws a `SireError` when running it from Sire release version 2023.0.0
The command I used is: `waterswap -c ../…