issues
search
prody
/
coMD
This package runs collective molecular dynamics simulations, where collective motions from anisotropic network model normal mode analysis drive all-atom dynamics through targeted molecular dynamics simulations and energy minimization
http://prody.csb.pitt.edu/comd/
MIT License
1
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Add support for nucleic acids
#78
jamesmkrieger
opened
2 years ago
0
Add support for externally built systems e.g. from CHARMM-GUI
#77
jamesmkrieger
opened
4 years ago
0
Fix issues with different VMD/AutoPSF versions
#76
jamesmkrieger
opened
4 years ago
0
Check/Add support for glycans
#75
jamesmkrieger
opened
4 years ago
0
Revert "added pbc unwrap in case of pbc problems"
#74
jamesmkrieger
closed
4 years ago
0
added break condition for number of retries exceeding 5
#73
jamesmkrieger
closed
4 years ago
0
fixed inconsistent minimisation length between walker1 and walker2
#72
jamesmkrieger
closed
4 years ago
0
added pbc unwrap in case of pbc problems
#71
jamesmkrieger
closed
4 years ago
0
reordered comd.tcl input args to move run_now up
#70
jamesmkrieger
closed
4 years ago
0
formatting fix
#69
jamesmkrieger
closed
4 years ago
0
added num_cores checking for Mac
#68
jamesmkrieger
closed
4 years ago
0
bug fix for someone leaving a space when entering chain ID
#67
jamesmkrieger
closed
4 years ago
0
bug fix on alternatives for having or lacking a GPU
#66
jamesmkrieger
closed
4 years ago
0
Structure B gets stuck and the CoMD run finishes
#65
jamesmkrieger
opened
4 years ago
0
added alternatives for not having +devices in the NAMD version
#64
jamesmkrieger
closed
4 years ago
0
bug fix at line 1377
#63
jamesmkrieger
closed
4 years ago
0
coMD - walker 2 TMD problem in comd.tcl
#62
abvl
closed
4 years ago
10
Error with coMD in VMD re GPUs
#61
roger99shi
opened
4 years ago
8
pass anmmc parameter to tcl file as values
#60
jamesmkrieger
closed
4 years ago
0
bug fix for initial minimization for walker 2
#59
jamesmkrieger
closed
5 years ago
0
documentation fix
#58
jamesmkrieger
closed
5 years ago
0
Reverted uniform mode amplitude
#57
jamesmkrieger
closed
5 years ago
0
continued fix
#56
jamesmkrieger
closed
5 years ago
0
Actual fix to double weighting and inclusion of Martini to anmmc.py
#55
jamesmkrieger
closed
5 years ago
0
bug fix for large systems
#54
jamesmkrieger
closed
5 years ago
0
bug fix for user specified GPUs and core
#53
jamesmkrieger
closed
5 years ago
0
bug fixes for anmmc to run
#52
jamesmkrieger
closed
5 years ago
0
Error with CoMD in VMD re autopsf
#51
rakeshr10
opened
6 years ago
5
reverted termination conditions and some other things
#50
jamesmkrieger
closed
6 years ago
0
multiple fixes
#49
jamesmkrieger
closed
6 years ago
0
made rmsd file readable during runs and bug fix for two PDBs and one GPU
#48
jamesmkrieger
closed
6 years ago
0
Aj comd/master
#47
jamesmkrieger
opened
6 years ago
0
bug fix for two PDBs and one GPU
#46
jamesmkrieger
closed
6 years ago
0
bug fix for two PDBs and one GPU
#45
jamesmkrieger
closed
6 years ago
0
pseudoatoms added
#44
JaviMota
closed
6 years ago
0
added rmsd file
#43
jamesmkrieger
closed
6 years ago
0
reversed decision to seed accept_para with accept_ratio
#42
jamesmkrieger
closed
6 years ago
0
working version again
#41
jamesmkrieger
closed
6 years ago
0
error handling changes
#40
jamesmkrieger
closed
6 years ago
0
fixed parameter order and renamed sh files for reporting
#39
jamesmkrieger
closed
6 years ago
0
added CPU counting
#38
jamesmkrieger
closed
6 years ago
0
Better error handling
#37
jamesmkrieger
closed
6 years ago
0
error checking for files after ANM-MC step
#36
jamesmkrieger
closed
6 years ago
0
Actual fix on parameter order that was attempted in minor fix
#35
jamesmkrieger
closed
6 years ago
0
bug fix
#34
jamesmkrieger
closed
6 years ago
0
bug fixes
#33
jamesmkrieger
closed
6 years ago
0
fixed error reporting
#32
jamesmkrieger
closed
6 years ago
0
Working version again
#31
ajimoreno
closed
6 years ago
0
bug fix
#30
jamesmkrieger
closed
6 years ago
0
bug fix
#29
jamesmkrieger
closed
6 years ago
0
Next