Commits · cc444b68c490347e7a53369b4686dc8b7aef486b · tbgl / tools / mrdna

Jun 14, 2018
- tmp commit of older work; changed how duplicate bonds are handled · 2175845a
  cmaffeo2 authored 6 years ago
  
  2175845a
- Likely fixed most backmapping bugs · cf915a07
  cmaffeo2 authored 6 years ago
  
  cf915a07
- Conditionally update coordinates using linear interpolation when there are not many beads · b670c7f0
  cmaffeo2 authored 6 years ago
  
  b670c7f0
- Fixed numerous bugs relating to strand routing · 9063e58f
  cmaffeo2 authored 6 years ago
  
  9063e58f
- Improved scripts for building cadnano structures; seems it will be neccesary... · 2bd05afb
  cmaffeo2 authored 6 years ago
  
  Improved scripts for building cadnano structures; seems it will be neccesary to make contour go from nt[0]-0.5 to nt[-1]+0.5
  2bd05afb
Apr 09, 2018
- Brough in some changes to cadnano_segments.py from origamitwo server · 70017fbc
  New Tbgl User authored 6 years ago
  
  70017fbc
Apr 07, 2018
- Added cadnano_segments · 51d8dde5
  cmaffeo2 authored 6 years ago
  
  51d8dde5
Dec 21, 2017
- Fixed run.py · 1b27f431
  cmaffeo2 authored 7 years ago
  
  1b27f431
Dec 20, 2017

Updated run script to remove unneeded simulation steps and make... · 2366e578

cmaffeo2 authored 7 years ago

Updated run script to remove unneeded simulation steps and make fine-resolution model run longer; also added dependency on pynvml to query gpus

2366e578

Aug 30, 2017
- Ordered GPUs according to PCI_BUS_ID in arbd/namd calls · d488dd39
  cmaffeo2 authored 7 years ago
  
  d488dd39
Aug 11, 2017
- Updated run script to use smaller rmsd · 96e539b8
  cmaffeo2 authored 7 years ago
  
  96e539b8
Jul 24, 2017
- Small updates to run script, flushing output of beadmodel · f584d0d1
  cmaffeo2 authored 7 years ago
  
  f584d0d1
Jul 20, 2017
- Updated run.py to use average coordinates · 39736a40
  cmaffeo2 authored 7 years ago
  
  39736a40
Jul 13, 2017
- Run script catches error when sequence is too short, falls back to random sequence · cc547bea
  cmaffeo2 authored 7 years ago
  
  cc547bea
Jul 12, 2017
- Increased bead model bond max length; fixed small bugs; improved handling of simulation output · d653044e
  cmaffeo2 authored 7 years ago
  
  d653044e
- Fixed problems with ENM for atomic model · 0eeb09e7
  cmaffeo2 authored 7 years ago
  
  0eeb09e7
- Fixed routines for removing long bonds; added CG sim w/o long bonds; various other minor changes · 1ee876af
  cmaffeo2 authored 7 years ago
  
  1ee876af
Jul 10, 2017
- Fixed small issues with atomicModel.py; parallelized run.py; removed old json files · a5f8294f
  cmaffeo2 authored 7 years ago
  
  a5f8294f
Jul 07, 2017
- Added atomicModel.simulate() · bc73ba71
  cmaffeo2 authored 7 years ago
  
  bc73ba71
- Fixed numerous small issues with atomic simulations; works now for pointer · f516c31e
  cmaffeo2 authored 7 years ago
  
  f516c31e
Jun 26, 2017
- Renamed function for removing long bond; function now works for ssDNA · c5253f62
  cmaffeo2 authored 7 years ago
  
  c5253f62
- Added 2 bead/bp model · a63e83b9
  cmaffeo2 authored 7 years ago
  
  a63e83b9
May 31, 2017
- Fixed assignment of atomic coordinates based on nucleotide position · aa67524b
  cmaffeo2 authored 7 years ago
  
  aa67524b
Apr 10, 2017
- Modified run script · 0c60adaa
  cmaffeo2 authored 7 years ago
  
  0c60adaa
Apr 07, 2017
- Seems to work · babbe87b
  cmaffeo2 authored 7 years ago
  
  babbe87b
- tmp · 28f29a88
  cmaffeo2 authored 7 years ago
  
  28f29a88