Amber-MD cpptraj issues

Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.

Other

138 stars 64 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Allow atommap rmsfit to proceed with partial atom maps

#1114 drroe opened 2 weeks ago
0
Fix parallel handling of data in repeated trajectory runs for 'rotate' and 'average'

#1113 drroe closed 2 weeks ago
0
Fix handling of generated rotation matrix sets in parallel with the 'rotate' command

#1112 drroe closed 3 weeks ago
0
Improve atom mapping between chiral centers

#1111 drroe closed 1 month ago
0
Doing a new release?

#1110 xiki-tempula opened 1 month ago
0
Add energy decomposition (with PME)

#1109 drroe closed 1 month ago
0
Multidihedral pca -> sidechain pca?

#1108 H-EKE opened 1 month ago
0
Cumulative radial distribution function

#1107 Saqlain5565 opened 1 month ago
0
Can CPPTRAJ read the dat file which is produced by other tool?

#1106 MilesYyh closed 1 month ago
5
Implement ability to calculate vector magnitude in 'vectormath' command.

#1105 drroe closed 1 month ago
0
Export dataset based on maths and distances

#1104 H-EKE closed 1 month ago
2
Puzzled by atom-based masking of energies

#1103 mkgilson closed 2 weeks ago
2
Attempt to fix pytraj test.

#1102 drroe closed 2 months ago
3
Add 'rescut' and 'bondoffset' keywords to 'prepareforleap'

#1101 drroe closed 2 months ago
0
Minor fix for PSF with NUMLP

#1100 drroe closed 2 months ago
1
Recognize Drude particles, improve handling of lone pairs

#1099 drroe closed 2 months ago
5
Test compatibility with Drude trajectories

#1098 drroe closed 2 months ago
4
Should multidihedral allow pseudo dihedrals?

#1097 drroe opened 3 months ago
0
Average structure not being distributed to all ranks in parallel

#1096 drroe closed 2 weeks ago
1
Creating mass-weighted covariance matrix

#1095 fatih4534 opened 4 months ago
3
Update CUDA support

#1094 drroe closed 4 months ago
0
Fix compilation on ARM based systems

#1093 drroe closed 4 months ago
1
Add 'addatom' action

#1092 drroe closed 4 months ago
1
Fix which atoms are reported in DSSP "missing atoms" warning message

#1091 drroe closed 4 months ago
1
Res TYR:1063 is missing atoms N

#1090 H-EKE closed 4 months ago
4
vector definition

#1089 H-EKE closed 4 months ago
5
Handle blank lines at the end of Karplus data file for jcoupling action

#1088 drroe closed 5 months ago
5
clang 15.0.7: testp.cpp:2:14: error: use of undeclared identifier 'printf'

#1087 hainm closed 5 months ago
3
CIF fixes, preserve CHARMM PSF segment ID

#1086 drroe closed 5 months ago
1
Add --disable-nczarr flag to netcdf configure

#1085 drroe closed 5 months ago
1
lDDT measure

#1084 rodrigogalindo opened 6 months ago
0
Error: No reference atoms selected for parm , [@CA]

#1083 H-EKE closed 3 months ago
16
Fix ambpdb build

#1082 drroe closed 6 months ago
0
Fix detection of NAMD-style unit cell parameters for NAMD DCD

#1081 drroe closed 6 months ago
0
Fix automatic identification of CIF files.

#1080 drroe closed 6 months ago
0
Add 'byfac' keyword to change mass/charge command

#1079 drroe closed 6 months ago
0
K-means++ Style initialization

#1078 drroe opened 6 months ago
0
Add ability to offset charge/mass, save charge/mass to variables

#1077 drroe closed 6 months ago
0
Fixes for'atommap'

#1076 drroe closed 6 months ago
0
Add TICA, max/min distance calc, and data projection commands

#1075 drroe closed 7 months ago
0
'atommap' command unexpected result

#1074 juan-alcantara1 closed 6 months ago
8
cpptraj

#1073 H-EKE closed 5 months ago
6
running multiple analysis in single file question

#1072 groponp closed 6 months ago
4
Install cpptraj las version

#1071 groponp closed 6 months ago
10
Problems on ARM systems

#1070 drroe closed 3 months ago
2
WIP - Playing with conda env for now (DO NOT MERGE)

#1069 hainm closed 8 months ago
8
Do not use "bad" box info from PDB files

#1068 drroe closed 8 months ago
3
Add command line flag to calculate charge

#1067 drroe closed 9 months ago
0
Add ability to extract box information to a data set

#1066 drroe closed 9 months ago
1
Selecting second molecule

#1065 almeida85 closed 6 months ago
3