-
## Description
We would like to enable simulations of very large systems (>4B particles), as well as their initialization. In a two stage approach, we should address breaking changes for the user i…
-
=========================================================================== ERROR: ACPYPE FAILED: No mod…
-
## Expected behavior ##
Analysis modules follow standard behavior, i.e., use [AnalysisBase](https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html) when possible.
## Actual be…
-
Dear All,
I am trying to install pyemma on a MAC M1 laptop with Python 3.10.6. I have tried various installation procedures and nothing seems to be working. Below are the outputs of different proce…
-
Hi Folks,
**Is your feature request related to a problem? Please describe.**
Feature/documentation request
We are running simulations of various SARS-CoV-2 proteins. There are certain simulat…
-
Hi,
Recently I have had to work with merged molecules, where the two endstates are not necessarily nicely input in the same conformation, but are instead taken from equilibrated structures which ma…
-
Currently `libcns` supports various restraints but only `ambig` is written via the `prepare_cns_input` function, we should thus refactor this function to take all possible restraints into account when…
-
HOOMD's tabulated potential implementation and API are being very widely used. Their implementation, and Python API in particular, could use a thorough review and be improved if possible.
-
Dear BioSimSpace developers:
I'm turning a hydrogen atom into a methyl group as the following picture shown (the red box), but there is an improper term about the green-labeled atoms in the ge…
kexul updated
2 years ago
-
Dear Moltemplate users,
I have an issue about " There are no atoms in the system".
I build a force-field of PDMS. The force field include atoms I need inside. (The partial code is shown below:) …