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For example `wrfout_d02_2010-01-29_22:20:00` is 52.6 GiB in size. This presents problems as our cloud backup solution only can handle 15 GiB files and we'd like to have all these on one filesystem at…
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Dear Khalak,
I found there are many clashes when aligning the decoupled structures of ligands in solvent into the apo state pocket. And some of them cannot be solved by just do a minimization and t…
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I've been observing very different `protocol_work` distributions when swapping between the old standalone `alchemy` package and the newer `openmmtools.alchemy`.
To illustrate the difference, I set…
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`pdbfixer` seems to produce a highly deformed structure for PDB id code `1AO7`.
You can reproduce this yourself by running the HTML-based `pdbfixer` on `1AO7` to simply build in the hydrogens. For s…
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Need to find a robust way to automate the mapping of BOINC Device numbers to physical card by Linux card number or pcie ID.
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Hi everyone,
In this project, we have a bunch of experimental data on the binding of small molecules to WDR91. Many of the molecules are in nice matched pairs, in which the molecules differ by a si…
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Is it possible to run OpenMM with a "regular" FF that is just modified by adding atom-centered point polarizabilities, or can these polarizabilities be used only in the context of the full AMOEBA FF?…
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Hello guys,
@andrewdurkiewicz @ion201 @orbeckst So our problem is that we have a PDE to solve which is second ordered in space and first ordered in time. I was thinking that we should use the techn…
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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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We've observed cases in which using too heavy of a hydrogen mass can cause too much mass to be subtracted from the parent heavy atom, causing instabilities instead of preventing them.
Instead, incr…