merge back the updated content - #55

Merged

jimboid merged 39 commits into

mainfrom

Oct 1, 2026

Commits on Jul 22, 2026

Create tw26 branch and populate OPENMM folder from CompBioAsia
CharlieLaughton
committed
ab675f0

Commits on Jul 28, 2026

Add links to AMBER and OpenMM in README
CharlieLaughton
authored
4661bf5

Commits on Jul 30, 2026

Merge pull request #1 from CCPBioSim/tw26
CharlieLaughton
authored
afb8227

Commits on Sep 2, 2026

First edit for training week 2026
CharlieLaughton
committed
8214ff4

Commits on Sep 9, 2026

update amber tutorial with abl-ligand system
jkalayan
committed
41be32b
add env and run script to root
jkalayan
committed
2cf57d6
fix formatting of amber output
jkalayan
committed
cc7d2a1
fix2 formatting of amber output
jkalayan
committed
2409865

Commits on Sep 21, 2026

update .py to work as https://github.com/CompBioAsia/mdme/blob/main/mesmy.sh, reduce nsteps for eq and prod steps
jkalayan
committed
80c40f7
update amber exec with pmemd.mpi
jkalayan
committed
1ea2b66
clean up comments
jkalayan
committed
0dcf14e
use args to generate bash script, add temp as arg
jkalayan
committed
223979b
add the amber executable as an arg
jkalayan
committed
a63e808
Merge pull request #2 from CCPBioSim/main
jimboid
authored
1858895

Commits on Sep 23, 2026

update default executable to sander.MPI from pmemd
jkalayan
committed
8e77e27
Merge branch 'main' of https://github.com/CCPBioSim/tw2026-protein-simulation-workshop
jkalayan
committed
f400b4e
use sander instead of pmemd for first two steps
jkalayan
committed
daf39f7
tidy up env setup script
jkalayan
committed
5487045
Remove duplicate env file.
jkalayan
committed
0340a12
Refactor Dockerfile for dependency installation
jimboid
authored
c973693
Add script to fix nglview version mismatches
jimboid
authored
36cbf21
Update latest badge URL in README.md
jimboid
authored
a5f8094
Disable test runs in build workflow
jimboid
authored
66a98ab
Delete .github/dependabot.yml
jimboid
authored
8778da2
Add Renovate configuration file for dependency management
jimboid
authored
3a93c10
Update Dockerfile
jimboid
authored
f952b80
add code to interate over sim frames with nglview
jkalayan
committed
98405c0
Add alternative instructions for sim viz
jkalayan
committed
d6ae666

Commits on Sep 24, 2026

Commits on Sep 25, 2026

reduce nsteps for OpenMM section and include matplotlib/pandas as dependencies
jkalayan
committed
f5a21ba
fix typo
jkalayan
committed
32c459c
Update Dockerfile
jimboid
authored
42627a0
Update Dockerfile
jimboid
authored
12a26c9

Commits on Oct 1, 2026

Uncomment test execution steps in build workflow
jimboid
authored
52b9620
Update pytest command to include OPENMM directory
jimboid
authored
11a5c6d
Merge pull request #4 from CCPBioSim/testing
jimboid
authored
43fbc32