Commits · 385f358ce2b4e95d01f5c30b72eca5628a6c6643 · tbgl / tools / mrdna

Feb 21, 2020
- Option and commands to convert crossovers into intrahelical · 385f358c
  cmaffeo2 authored 5 years ago
  
  385f358c
- Made minimum automatic dimensions 1000 · e4583787
  cmaffeo2 authored 5 years ago
  
  e4583787
- Added easy commands for ignoring long bonds during coarse-simulation · aacf4cba
  cmaffeo2 authored 5 years ago
  
  aacf4cba
Jan 02, 2020
- Optionally run enrg-md simulations · f9d7ee2b
  cmaffeo2 authored 5 years ago
  
  f9d7ee2b
Dec 12, 2019
- Set origin of arbd box using structure in mrdna script · 47b578f2
  cmaffeo2 authored 5 years ago
  
  47b578f2
Dec 06, 2019
- mrdna script now recognizes list files for model creation · 11161c71
  cmaffeo2 authored 5 years ago
  
  11161c71
Nov 18, 2019
- Updated mrdna script to use dimensions of object for system · c6e082b9
  cmaffeo2 authored 5 years ago
  
  c6e082b9
Aug 20, 2019
- Added temperature argument to mrdna · bd969cce
  cmaffeo2 authored 5 years ago
  
  bd969cce
Aug 13, 2019
- Added 'fix_linking_number' option to mrdna script; fixed bug in --debug option · 5bd0d211
  cmaffeo2 authored 5 years ago
  
  5bd0d211
Jul 10, 2019
- Added ability to adjust screening length · 47325593
  cmaffeo2 authored 5 years ago
  
  47325593
Feb 01, 2019
- Initial implementation of export to oxDNA · 0ca4dc50
  cmaffeo2 authored 6 years ago
  
  View commits for tag 0.3 0.3
  
  0ca4dc50
Dec 02, 2018

Slightly reorganized simulation protocol; added options to mrdna script and... · 73c13369

cmaffeo2 authored 6 years ago

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step

73c13369

Oct 01, 2018
- Automated versioning · 0ea91b45
  cmaffeo2 authored 6 years ago
  
  View commits for tag 0.2 0.2
  
  0ea91b45
Sep 28, 2018
- Added _user_requested_quit to debug mode for mrdna script · 0e3c7a68
  cmaffeo2 authored 6 years ago
  
  0e3c7a68
Sep 27, 2018
- Added --debug option to mrdna script · f942e555
  cmaffeo2 authored 6 years ago
  
  f942e555
Sep 25, 2018
- Fixed handling of --draw-* arguments for mrdna script · 3d3db5dd
  cmaffeo2 authored 6 years ago
  
  3d3db5dd
- Fixed script handling of multiple suffixes · 947532fa
  cmaffeo2 authored 6 years ago
  
  947532fa
Sep 23, 2018
- Added tube representation · 9f582572
  cmaffeo2 authored 6 years ago
  
  9f582572
Sep 18, 2018
- added drawing cylinder option to mrdna · 89de52da
  dwinogra authored 6 years ago
  
  89de52da
Sep 17, 2018
- Updated simulate.py to fix ENM name, copy force field · d9626894
  cmaffeo2 authored 6 years ago
  
  d9626894
Sep 11, 2018
- Added support for reading in orientation; added enrgmd script for output... · 7ccbb105
  cmaffeo2 authored 6 years ago
  
  Added support for reading in orientation; added enrgmd script for output enrgmd files without running simulations
  7ccbb105
Sep 05, 2018
- Renamed project to 'mrdna' · d291aa85
  cmaffeo2 authored 6 years ago
  
  d291aa85
- Updated dnarbd script to allow specification of the output period · 135db759
  cmaffeo2 authored 6 years ago
  
  135db759
Sep 04, 2018
- Updated dnarbd script to better handle number-of-step arguments such as '1e7' · fe860000
  cmaffeo2 authored 6 years ago
  
  fe860000
- Updated dnarbd script to use pathlib and to use file's basename rather than full path · 1b3ad2f1
  cmaffeo2 authored 6 years ago
  
  1b3ad2f1
Aug 29, 2018
- polygon_mesh: Changed bead positions at crossovers to fix issue with single-nt polymers · a83baf1b
  cmaffeo2 authored 6 years ago
  
  a83baf1b
Aug 28, 2018
- Added dnarbd binary to repository for command line invocation · fdc21600
  cmaffeo2 authored 6 years ago
  
  fdc21600