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The file format should support common input and output for these applications:
At minimum:
1. Molecular dynamics: simulation (OpenMM, DESMOND, etc.) and analysis packages (MDTraj, PyTraj, etc.)
2. Qu…
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Spinoff discussion from https://github.com/openmm/openmm/issues/3924
This issue is to discuss whether we can port the AIREBO force field from LAMMPS (https://arxiv.org/pdf/1810.07026.pdf) and the f…
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Hi,
I am trying to calculate apl for different lipids in a coarse grained bilayer with a receptor.
However I get the error:
Traceback (most recent call last):
File "/mnt/software/python2.7/lib/…
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2012 Cahill: "Of the four main phospholipids in membranes, threephosphatidylethanolamine (PE), phosphatidylcholine (PC), and sphingomyelin (SM)—are neutral, and one, phosphatidylserine (PS), is negati…
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Hello experts,
I've been trying to run simulations of proteins with a hybrid, both explicit+implicit, solvent model, but don't really know what is the right way to define the forcefield.
It is …
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what is the difference between "import molgen" and "from poetry import molgen" ?
first one is more likely old code from GALAMOST,
in the new pygamd, it shows error when I run "from poetry import mol…
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thank you very much I managed to install without cuda however it doesn't load hip and only loads opencl
I tested the following linux kernels : 5.15.0-52-generic , 6.0.3-060003-generic on Ub…
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It would be good to have some fleshed out use cases to understand what this file format will (and won't!) support. Here's a brainstormed list that probably reflects my biases:
Biomolecular
- A protei…
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I am running temperature replica exchange simulations on small coarse-grained oligomer systems (containing a single chain), and have been using an ensemble validation check on the energies for thermod…
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## Keyword: out of distribution detection
There is no result
## Keyword: out-of-distribution detection
There is no result
## Keyword: expected calibration error
There is no result
## Keyword: overc…