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Thank you for your great work on this library @Gabri95! I observed some behavior regarding the implemented `R2` convolution layer and was wondering if you know why this is happening.
I'm using the …
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`write_gsd` doesn't work if masses aren't set in the topology.
```
129 masses = np.array([site.mass for site in top.sites])
130 masses[masses == 0] = 1.0
--> 131 gsd_snapshot.particles.mass…
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### Bug summary
run pbsa compute successfully, but an error occur when compute nmode entropy.
Error is "Found an invalid periodicity in the prmtop file: 60"
I have noted that, : pbsa compute vi…
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A vertical tail wing (of an aircraft, NACA 0012) is simulated in OpenVSP, 3.27.1-win64.
The angle in z (deflection) is changed from -10° to +10°
One would expect the results to be symmetric, however…
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Hi
I am using ProDy for the first time. I tried submitting job for PCA using ProDY plugin in VMD. In last line it shows an error (see below), but It generated three files; .dcd file, .pdb file and .…
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**Describe the bug**
It seems that I cannot run the xtb when numpy is installed at the same time.
**To Reproduce**
I create the environment with the script
```
>>> environment.yml
name: test…
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Chris Chipot reported via email that there are systematic inaccuracies encountered by @HanatoK in the computation of total forces using MTS (i.e. presumably, with `timeStepFactor` > 1). @HanatoK feel…
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In `main.py` the `_cmd_receive_dd ` string is used to unpack the return values of `domain_decomposition`.
However, all the variables (`positions`, `velocities`, `indices`, etc) are local to the `main…
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Currently, the Ramachandran plotter program requires the installation of the Phenix Suite in order to generate dihedral angles of the user's given protein. This is being changed to remove the reliance…
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Hi,
So I was defining link information for backbone bonds, angles and dihedrals under the link directive as follows but this information do not show up in the molecule.itp file. Is this a bug or am …