Commits · 4feb04dba44280a38225b815a6686bf192fc684b · tbgl / tools / mrdna

Dec 21, 2017
- Removed assertion that numSteps must be of type 'int' · 12a7248f
  cmaffeo2 authored 7 years ago
  
  12a7248f
Aug 31, 2017
- Made neighborhood for bead model backmapping dynamically increase if needed · 6dcc8f64
  cmaffeo2 authored 7 years ago
  
  6dcc8f64
- Reduced pairlist distance in ARBD models · 72bfa8fb
  cmaffeo2 authored 7 years ago
  
  72bfa8fb
Aug 30, 2017
- Ordered GPUs according to PCI_BUS_ID in arbd/namd calls · d488dd39
  cmaffeo2 authored 7 years ago
  
  d488dd39
Aug 11, 2017
- Removed random seed from bead models · 873aa76a
  cmaffeo2 authored 7 years ago
  
  873aa76a
Aug 02, 2017
- Updated pdb writers so resid is left justified, system dimensions are 1000 AA · 3268d1e7
  cmaffeo2 authored 7 years ago
  
  3268d1e7
Jul 24, 2017
- Small updates to run script, flushing output of beadmodel · f584d0d1
  cmaffeo2 authored 7 years ago
  
  f584d0d1
Jul 20, 2017

Updated bead model handling of extra interhelical bonds due to crossovers... · f864b0cf

cmaffeo2 authored 7 years ago

Updated bead model handling of extra interhelical bonds due to crossovers between distant segments; now works for single crossovers

f864b0cf

Jul 18, 2017
- Fixed NBONDS in psf writers for bead models · 7c1baa78
  cmaffeo2 authored 7 years ago
  
  7c1baa78
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 routines for removing long bonds; added CG sim w/o long bonds; various other minor changes · 1ee876af
  cmaffeo2 authored 7 years ago
  
  1ee876af
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
Jun 15, 2017
- Added method for combining CG bead models · 27378a10
  cmaffeo2 authored 7 years ago
  
  27378a10
Jun 13, 2017
- Added logic to handle cases where bpsPerNode <= 0 (because of deletions) · 816ca1c5
  cmaffeo2 authored 7 years ago
  
  816ca1c5
Jun 08, 2017

Fixed beadModel neighborhood algorithm; Added atomicModel support for looped... · 3e857438

cmaffeo2 authored 7 years ago

Fixed beadModel neighborhood algorithm; Added atomicModel support for looped structures; Added methods for breaking bonds beyond a certain length

3e857438

May 31, 2017
- Fixed bug with node placement in 'diagonal' crossovers · 01308d38
  cmaffeo2 authored 7 years ago
  
  01308d38
- Improved neighborhood-finding routine for backmapping closed structures · 0ef3a432
  cmaffeo2 authored 7 years ago
  
  0ef3a432
May 29, 2017
- Several untested changes when building model; new handling of maxForce · 37bf35cf
  cmaffeo2 authored 7 years ago
  
  37bf35cf
- Fixed twist; increased twist Lp to 90nm; increased stiffnesss of 90deg... · 055f8ac7
  cmaffeo2 authored 7 years ago
  
  Fixed twist; increased twist Lp to 90nm; increased stiffnesss of 90deg crossover angle restraint; added .gitignore
  055f8ac7
Apr 10, 2017
- Increased dihedral angle stiffness · 8823d32d
  cmaffeo2 authored 8 years ago
  
  8823d32d
Apr 07, 2017
- Seems to work · babbe87b
  cmaffeo2 authored 8 years ago
  
  babbe87b
- Fixed bug in generating dihedrals · 09c03e6b
  cmaffeo2 authored 8 years ago
  
  09c03e6b
- tmp · 28f29a88
  cmaffeo2 authored 8 years ago
  
  28f29a88
- Made it possible to specify timestep; update k_spring for dihedrals · bdae7c9f
  cmaffeo2 authored 8 years ago
  
  bdae7c9f
Apr 05, 2017
- Added seperate neighborhood cutoffs for ssDNA; remove a little unused code · 84e036c7
  cmaffeo2 authored 8 years ago
  
  84e036c7
- Fixed handling of ssDNA crossovers in bead model · 687b59f7
  cmaffeo2 authored 8 years ago
  
  687b59f7
- Fixed some more backmapping problems · 4dc61b52
  cmaffeo2 authored 8 years ago
  
  4dc61b52
- Fixed some minor backmapping issues · 2031418e
  cmaffeo2 authored 8 years ago
  
  2031418e
- Fixed crossover bond lengths · 6c093a2e
  cmaffeo2 authored 8 years ago
  
  6c093a2e
- Atomic backmapping now works · bd4ec932
  cmaffeo2 authored 8 years ago
  
  bd4ec932
Apr 04, 2017
- Got backmapping to work · 4184f1d5
  cmaffeo2 authored 8 years ago
  
  4184f1d5
Apr 03, 2017
- Meerged branches · 6947ae05
  cmaffeo2 authored 8 years ago
  
  6947ae05
- Began renaming files for a unified beadModel class · 0d5bd967
  cmaffeo2 authored 8 years ago
  
  0d5bd967
Mar 29, 2017
- Weakened crossover angle potentials and extended intrahelical exclusions · 5bc042f9
  cmaffeo2 authored 8 years ago
  
  5bc042f9
- Fixed fwd/rev shift in dihedral; extended getDihedrals to allow all crossovers... · 1dc79c61
  cmaffeo2 authored 8 years ago
  
  Fixed fwd/rev shift in dihedral; extended getDihedrals to allow all crossovers within a distance; increased crossover angle spring constant
  1dc79c61
Mar 27, 2017

Added more complex nb types; increased intrahelical bond spring constant;... · 98f89a81

cmaffeo2 authored 8 years ago

Added more complex nb types; increased intrahelical bond spring constant; tried and commented out increased angle spring constant; nothing really helped

98f89a81

Mar 26, 2017
- Fixed dihedrals, I think · af527873
  cmaffeo2 authored 8 years ago
  
  af527873
Mar 01, 2017

Adjusted twist Lp to 200 nm and non-bonded parameters until pointer relaxed... · 34b403f9

cmaffeo2 authored 8 years ago

Adjusted twist Lp to 200 nm and non-bonded parameters until pointer relaxed realistically; added support for angles to crossover connections

34b403f9

Feb 28, 2017
- Fixed treatment of dihedral angles, increased twist persistence length to 75 again · bec587ee
  cmaffeo2 authored 8 years ago
  
  bec587ee