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Swarm-CG
Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
https://pubs.acs.org/doi/10.1021/acsomega.0c05469
MIT License
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Swarm-CG
#48
webridging
closed
1 week ago
0
Newer gromacs version than 2019 have a different tpr and are not supported?
#47
BartBruininks
closed
5 months ago
1
MD run failed(unstable simulation was killed, with unstable = NOT writing in log file for 60 sec)
#46
zdworld
opened
10 months ago
0
md run failing
#45
summer-noon
opened
1 year ago
0
"CG ITP file constraints have been grouped, but constraints group 1 holds lines that have different parameters"
#44
StefanoMuscat
opened
2 years ago
1
[TypeError: center() got an unexpected keyword argument 'pbc']
#43
kurokawaikki
opened
2 years ago
7
Swarm-CG & Gromacs 2021
#42
Maryam-Sadeghi
opened
3 years ago
0
Constraints optimization
#41
MaksimKalutskiy
closed
3 years ago
3
Reorganize test files
#40
giovannidoni
closed
3 years ago
0
Add input class
#39
giovannidoni
closed
3 years ago
0
Store default input file inside repository
#38
giovannidoni
closed
3 years ago
0
Add docstring to remaining bits and clean up formatting
#37
giovannidoni
closed
3 years ago
0
Add ns attr docstrings
#36
giovannidoni
closed
3 years ago
1
Enable simulation parameter editing
#35
giovannidoni
closed
3 years ago
2
Move argument formatting
#34
giovannidoni
closed
3 years ago
1
WIP: Move arguments formatting
#33
giovannidoni
closed
3 years ago
0
scg_optimize fails on WSL due to permission denied
#32
maurobedoya
opened
3 years ago
1
Move sim settings
#31
giovannidoni
closed
3 years ago
1
Add gmx link in base image and add commands to run
#30
giovannidoni
closed
3 years ago
0
First implementation end2end
#29
giovannidoni
closed
3 years ago
1
Validation
#28
giovannidoni
closed
3 years ago
0
Apply decorator
#27
giovannidoni
closed
3 years ago
0
Add decorator to handle warnings
#26
giovannidoni
closed
3 years ago
0
Add method for checking exec and tests, move eval_function
#25
giovannidoni
closed
3 years ago
0
Io cleanup check
#24
CharlyEmpereurmot
closed
3 years ago
0
Io cleanup
#23
giovannidoni
closed
3 years ago
0
Add basic integration test scripts
#22
giovannidoni
closed
3 years ago
0
Small corrections
#21
CharlyEmpereurmot
closed
3 years ago
0
Runner
#20
giovannidoni
closed
3 years ago
2
Group scoring functions
#19
giovannidoni
closed
3 years ago
0
Extended Usage Request: Adding GROMACS angle function 10 - Restriced Bending Angle Potential
#18
mikeboyle321
opened
3 years ago
1
AttributeError: 'Namespace' object has no attribute 'gmx_cmd'
#17
mikeboyle321
closed
3 years ago
3
Corrected limits on force constants + Better explanations in the help
#16
CharlyEmpereurmot
closed
3 years ago
0
Fixed help description
#15
CharlyEmpereurmot
closed
3 years ago
0
Fixed scg_evaluate
#14
CharlyEmpereurmot
closed
3 years ago
0
Fixed -user_params for nb_particles < 3
#13
CharlyEmpereurmot
closed
3 years ago
0
Add option to consider prelim. user parameters instead of just using Direct Boltzmann Inversion
#12
CharlyEmpereurmot
closed
3 years ago
0
Allow using initial model parameters
#11
CharlyEmpereurmot
closed
3 years ago
0
not listed on the MDAnalysis "Used by" page
#10
orbeckst
closed
3 years ago
1
Updating Develop to Master 9.10.2020
#9
fiskissimo
closed
3 years ago
0
Usage of virtual sites and better compatibility with MARTINI 3
#8
CharlyEmpereurmot
closed
3 years ago
0
Added handling of virtual sites + Fixed an issue in BI
#7
CharlyEmpereurmot
closed
3 years ago
0
Add exceptions
#6
giovannidoni
closed
3 years ago
0
Cleanup03
#5
giovannidoni
closed
3 years ago
0
Cleanup02
#4
giovannidoni
closed
3 years ago
0
Add gititnore and codeowners
#3
giovannidoni
closed
3 years ago
0
Cleanup 01
#2
giovannidoni
closed
3 years ago
0
VirtualSites are silently dropped from itp
#1
fgrunewald
opened
3 years ago
4