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Amber-MD
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cpptraj
Biomolecular simulation trajectory/data analysis.
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Improve unit cell detection for charmm trajectory (dcd) files
#1064
drroe
closed
10 months ago
0
If wildcard expansion fails in a list for loop, do not add to the loop.
#1063
drroe
closed
10 months ago
1
Pin the cython version. Does not appear to work with cython 3.X.X.
#1062
drroe
closed
11 months ago
2
Fix the -DDEBUG compile
#1061
drroe
closed
11 months ago
2
Add ability to change names in 'atommap' command
#1060
drroe
closed
11 months ago
3
Add note about strip and atomicfluct with `pdbres` keyword
#1059
slochower
closed
11 months ago
3
Unable to Install pytraj from source code on Linux using cpptraj (Ubuntu 22.04.3 LTS)
#1058
PhiMykah
closed
11 months ago
2
Are the options for `parmopts` documented anywhere?
#1057
slochower
closed
11 months ago
16
Add 'mergeres' keyword to 'change' command
#1056
drroe
closed
12 months ago
0
Add MPI parallelism and rotatable grids to GIST
#1055
drroe
closed
1 year ago
1
Add 'charge' keyword to 'keep' and 'strip' to scale total charge of remaining atoms.
#1054
drroe
closed
1 year ago
0
Add ability to utilize and manipulate internal coordinates
#1053
drroe
closed
1 year ago
2
Add ability to scale charges with the 'graft' command
#1052
drroe
closed
1 year ago
1
Add extended similarity comparison functionality
#1051
drroe
closed
1 year ago
0
Minor typo
#1050
rodrigogalindo
closed
6 months ago
1
Adding Clustering via Extended Similarity Metrics
#1049
drroe
opened
1 year ago
5
Add change mass/charge command.
#1048
drroe
closed
1 year ago
0
WIP: Update merge-gate.yml - test pytraj build
#1047
hainm
closed
1 year ago
1
Add 'parsetiming' command
#1046
drroe
closed
1 year ago
14
Add Time Independent Correlation Analysis
#1045
drroe
closed
6 months ago
1
Distribution of the tetrahedral order parameter Q for TIP4P/2005
#1044
Saqlain5565
opened
1 year ago
0
Local structure index of water (LSI) code issue
#1043
Saqlain5565
opened
1 year ago
3
Add 'openmm' keyword to 'energy' action
#1042
drroe
closed
1 year ago
7
Fix segfault when performing a second run with a reference after reference structures have been cleared
#1041
drroe
closed
1 year ago
0
Fix bug in Ewald direct sum energies for smaller unit cells
#1040
drroe
closed
1 year ago
0
"reference" after "clear all" causes segmentation fault
#1039
gaborb91
closed
1 year ago
5
unit of force in Jarcynski ASMD output
#1038
macardosa
closed
1 year ago
2
Add ability to write axes, take user specified base pairs, and report all hydrogen bonds to nastruct
#1037
drroe
closed
1 year ago
1
NAStruct feature request: output axes info for bases and basepairs
#1036
tcbishop
opened
1 year ago
8
Try to add a pytraj GitHub Actions build job
#1035
drroe
closed
1 year ago
1
Fix parallel analysis when ensemble is active
#1034
drroe
closed
1 year ago
1
Allow reading of badly formatted PSF files
#1033
drroe
closed
1 year ago
1
Add diffusion calculation from multiple time origins and toroidal-view scheme
#1032
drroe
closed
1 year ago
2
Add check for intel MPI wrappers in configure script
#1031
drroe
closed
1 year ago
0
Add ability to remove NPT fluctuations in diffusion calculation
#1030
drroe
closed
1 year ago
0
Guidance required on MD simulation
#1029
Saqlain5565
closed
6 months ago
4
Add ability to remove box fluctuations when unwrapping NPT trajectories.
#1028
drroe
closed
1 year ago
1
Fix unwrapping and diffusion imaging for NPT trajectories
#1027
drroe
closed
1 year ago
1
Density out file from NPT
#1026
Saqlain5565
closed
1 year ago
7
Update version of NetCDF that CPPTRAJ will try to build.
#1025
drroe
closed
1 year ago
1
GIST Should have the option to write binary files
#1024
drroe
opened
1 year ago
0
cpptraj GIST stucks after 90% of results written
#1023
EgorBulavkoSk
closed
6 months ago
7
Query regarding mask option
#1022
saikat0003
closed
1 year ago
2
configure error
#1021
mayank-kohli
closed
11 months ago
13
new macos issue
#1020
hainm
opened
1 year ago
6
Miscellaneous cleanup
#1019
drroe
closed
1 year ago
1
Fixes for nastruct, ZDNA and parallel DNA
#1018
drroe
closed
1 year ago
3
Add codeql badge. Remove lgtm badge.
#1017
drroe
closed
1 year ago
3
Fix '*' wildcard matching.
#1016
drroe
closed
1 year ago
0
Fix xtalsymm command use of unit cell matrices
#1015
drroe
closed
1 year ago
2
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