proteneer/timemachine

Issues

• Can't pickle classes that define __getattr__

  #335 opened 4 years ago
  2

• Fix jax upgrade issue

  #333 opened 4 years ago
  2

• Improve performance of RBFE simulations

  #326 opened 4 years ago
  4

• clean up Observables class

  #321 opened 3 years ago
  2

• Optimize Distance Calculations

  #320 opened 3 years ago
  1

• Alchemically scale exclusions or turn off nonbonded interactions for multiple R-groups

  #313 opened 4 years ago
  2

• Improve single gpu performance

  #312 opened 4 years ago
  4

• Disable cub download in CMake on cuda 11.1

  #308 opened 4 years ago
  2

• Make u, du_dx and x_t internally consistent

  #306 opened 4 years ago
  5

• Upgrade jax

  #302 opened 4 years ago
  2

• Debug extremely large inertial restraint force

  #296 opened 4 years ago
  3

• Per target bias

  #282 opened 3 years ago
  1

• Protein Forcefield

  #281 opened 4 years ago
  0

• Running variance

  #280 opened 4 years ago
  2

• cap max nonbonded energy to deal with nonbonded exclusions

  #272 opened 4 years ago
  2

• Support for separated topologies.

  #271 opened 3 years ago
  1

• GPU hilbert sort

  #268 opened 4 years ago
  1

• Optimize nblist construction with __shfl

  #267 opened 4 years ago
  1

• Installation troubleshooting

  #266 opened 3 years ago
  7

• Optimizations

  #265 opened 4 years ago
  7

• Planning doc for some major upcoming changes

  #263 opened 4 years ago
  2

• reservoir sampling restoration

  #262 opened 4 years ago
  0

• Reaction field

  #260 opened 4 years ago
  1

• differentiable 4D minimization

  #258 opened 4 years ago
  2

• bootstrap estimators

  #255 opened 4 years ago
  1

• Multiplex backwards mode

  #250 opened 4 years ago
  1

• Stabilize LennardJones derivatives.

  #248 opened 4 years ago
  2

• Radially symmetric centroid based restraints

  #246 opened 4 years ago
  1

• Improve multi-node performance

  #245 opened 4 years ago
  4

• Add more debug information to each lambda window print out

  #243 opened 4 years ago
  1

• debug differences in free energies computed between am1ccc and am1bcc

  #231 opened 4 years ago
  0

• implement am1 cache

  #225 opened 4 years ago
  1

• anchor restraints to c-alpha backbone atoms as opposed to sidechains

  #224 opened 4 years ago
  1

• reduce file sizes

  #223 opened 4 years ago
  1

• switch to adam optimizer

  #222 opened 3 years ago
  1

• implement multiplexing

  #220 opened 4 years ago
  3

• Distributed discovery and registration

  #215 opened 4 years ago
  1

• cleanup simulation_v2 code for tabulating du_dls

  #212 opened 4 years ago
  2

• Print per force-type du/dl trapz differences

  #207 opened 5 years ago
  1

• Implement smooth switching functions for electrostatics and GB

  #206 opened 4 years ago
  1

• Parameter interpolation of valence terms

  #202 opened 4 years ago
  2

• fixed point madness

  #201 opened 4 years ago
  1

• context is nondeterministic

  #200 opened 5 years ago
  1

• Make GB energy continuous at cutoff

  #198 opened 4 years ago
  1

• interpolation

  #196 opened 5 years ago
  5

• Allow arbitrary cutoffs for nonbonded terms

  #193 opened 5 years ago
  3

• Bug in N_limit_ code

  #192 opened 5 years ago
  2

• List of todos for RBFE

  #186 opened 5 years ago
  1

• Switch to the adam optimizer

  #176 opened 5 years ago
  6

• Make PDB writing more robust.

  #174 opened 5 years ago
  2