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Hey everyone,
I hope you're all not too overwhelmed with all the changes to the GitHub repo lately! I've ran into a lot of extra time to focus on this work and brainstorm with @mrshirts since the end…
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I'm looking to perform some alchemical free energy calculations and recently started using OpenMM to do this. You've all done some nice work here, so I don't want to re-invent the wheel, but I initia…
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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This relates to #3229 and #3236. CustomNonbondedForce computes its long range correction based on the current values of global parameters. That means it must be recomputed every time a parameter cha…
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Issue #302, that enormous discussion that hovers around fexprs and Kernel but sometimes veers out into the unknown and asks really deep and important questions about computation itself (and how it's m…
masak updated
1 month ago
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How can we know if a pdb is going to be a good candidate for simulation? Are the initial conditions that stop us from being able to simulate? Estimate the total number of eligible candidates.
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Hello tom91136
I am trying do the miniBUDE)/sycl/ project and try to implement on opeapi. However i find the data files' content(.in file) from data/bm1 and data/bm2 are almost garbled text. May …
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Hi,
The demo.sh and variations have this argument:
--model-dir checkpoint_best.pt
This file does not exist. If I replace it by:
--model-dir ../weights/unimol_docking_v2_240517.pt
I get errors …
CLG68 updated
5 months ago
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Hi,
I am trying to use `yank` on 2 nodes with 2 GPU cards on each node.
I can sucessfully run `yank` example on a single node with 2 GPU cards. But when I run it on 2 nodes with 4 cards in tota…
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Hi Thomas,
Recently we have tested the CDPKit confgen for the astex and posebuster datasets. We curated the crystal structures for each of the ligands, apply some Glide-style fragmentation for the l…