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[Hayes, Joseph M., and Georgios Archontis. "MM-GB (PB) SA calculations of protein-ligand binding free energies." Molecular Dynamics-Studies of Synthetic and Biological Macromolecules (2012): 171-190](…
cramg updated
3 years ago
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I want to try to simplify the way standard state corrections are incorporated in Yank, and was hoping to get suggestions from @luirink and @davidlmobley.
For generality, Yank uses the concept of "pha…
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> We could use some more quantitative analysis of binding free energy, like FEP (free energy perturbation). Will take a look in a few days when I have more time.
Hi, I agree. Our coll…
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- Currently, Custom label make use of `[label_options](https://github.com/e-mission/nrel-openpath-deploy-configs/tree/main/label_options)` to extract the CO2 emission calculations while there is no en…
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Default settings for a 200 ps equilibration simulation with a system of 50k atoms takes more than 24 hours to complete on a typical GPU cluster with an optimised Gromacs installation for Binding free …
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### Description
The function hoomd.update.RemoveDrift() currently updates the position of all particles in the simulation. I would like to be able to pass a subset of particles so that the center-of-…
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The memory requirements of TensErLEED (especially the refcalc) can become quite limiting when tackling large unit cell systems. @LutzHammer reported needing about 25 GB of memory per energy step in th…
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[Miller, Bill R, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, and Adrian E Roitberg. “MMPBSA.Py : An Efficient Program for End-State Free Energy Calculations.” *Journal of Chemical T…
cramg updated
3 years ago
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It would be useful to have a lightweight package for easily reading, interrogating, manipulating, and doing analysis of the JSON analysis files we generate from fah-xchem. To do this, we currently nee…
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Sim…
cramg updated
3 years ago