JuliaMolSim/Molly.jl

Issues

• How to cite?

  #146 opened 9 months ago by HLinde
  6

• UndefVarError: `σ6` not defined ERROR when simulating the NPT ensemble

  #169 opened 3 months ago by GDufenshuoo
  1

• Boundary Conditions

  #167 opened 4 months ago by StanleyN1
  1

• sys.coords does not work as Vector{Vector}

  #162 opened 4 months ago by ejmeitz
  2

• Molly needs a logo!

  #101 opened 2 years ago by JaydevSR
  13

• EAM implementation and dimension error

  #164 opened 4 months ago by kangpyo
  5

• Should we have functions to add and remove atoms to/from a `System`?

  #152 opened 8 months ago by jgreener64
  3

• open an sdf file

  #154 opened 8 months ago by maartensandbox
  10

• return type for force for pairwise potential in CUDA

  #161 opened 6 months ago by nwalet
  1

• GPU error with the example

  #159 opened 6 months ago by nwalet
  4

• Units in Nose Hoover temperature

  #157 opened 7 months ago by nwalet
  1

• Molly.jl: AD with Enyzme returns 0 gradient

  #156 opened 7 months ago by pushingPulling
  1

• Example for new MC membrane barostat

  #141 opened a year ago by bondrewd
  12

• Should we pass more properties (e.g. velocities, step number) to `force`/`potential_energy`?

  #151 opened 8 months ago by jgreener64
  4

• [feature request] velocity-dependent forces

  #148 opened 9 months ago by algorithmx
  2

• Inconsistent Units Crash Simulation

  #135 opened 10 months ago by ejmeitz
  5

• AtomsBase not properly implemented

  #128 opened a year ago by mfherbst
  4

• apply_coupling! method is not found for custom coupling function

  #137 opened a year ago by HLinde
  2

• GPU error with custom pairwise interactions

  #134 opened a year ago by bondrewd
  5

• System constructor cannot be found?

  #112 opened a year ago by axsk
  3

• Boltzmann Constant in LAMMPS 'real' units does not work

  #127 opened a year ago by ejmeitz
  5

• Links in Docs are broken

  #126 opened a year ago by ejmeitz
  2

• key "HB1" not found in forcefield

  #124 opened a year ago by overshiki
  1

• Unit conversion for general interactions

  #121 opened a year ago by swyant
  5

• Differentiable GPU kernels

  #60 opened 2 years ago by jgreener64
  16

• GPU tests fail on GTX970 and P100

  #57 opened a year ago by leios
  7

• Access coordinates of different time steps and use it for differential learning.

  #47 opened a year ago by moradza
  4

• Automatic conversion to terminal N-terminal hydrogens

  #114 opened a year ago by axsk
  4

• Precompilation error due to zygote.jl

  #117 opened a year ago by Geophyte
  4

• Molly Feature Parity List

  #108 opened a year ago by ejmeitz
  1

• Symbol missing error when running documentation code

  #106 opened a year ago by ejmeitz
  1

• Incompatibility of types -> bug

  #103 opened 2 years ago by Leticia-maria
  2

• testing failure with CellListMap v0.8.3

  #102 opened 2 years ago by leios
  4

• Compilation failed for Julia 1.73 and 1.8 on Apple M1 chip

  #80 opened 2 years ago by jty-computation
  5

• `Mie` interaction gives `InexactError` due to the `convert` in constructor

  #94 opened 2 years ago by JaydevSR
  1

• Broken links in docs

  #92 opened 2 years ago by chemicalfiend
  2

• Dead link in force.jl

  #90 opened 2 years ago by jty-computation
  1

• Wrapping the interactions in a structure.

  #85 opened 2 years ago by JaydevSR
  2

• Precompilation error due to changes in Zygote.jl

  #79 opened 2 years ago by JaydevSR
  2

• Error in Testing of Molly.jl

  #78 opened 2 years ago by iajzenszmi
  3

• FENE bond and Cosine angle potential

  #73 opened 2 years ago by ehsanirani
  3

• Straight angle may produce NaNs in HarmonicAngle

  #58 opened 2 years ago by tverho
  1

• Inconsistency with AtomsBase interface

  #55 opened 2 years ago by jrdegreeff
  3

• Fix shifted force cutoff potential calculation

  #53 opened 2 years ago by noeblassel
  2

• Bug in KineticEnergyLogger

  #51 opened 2 years ago by jrdegreeff
  1

• Most of the examples has bugs with version 0.7.0

  #50 opened 2 years ago by skycolt
  0

• Request: clarifying units that Molly uses

  #39 opened 3 years ago by ehgus
  2

• Handling invalid numerical parameters

  #34 opened 3 years ago by jrdegreeff
  3

• Example protein simulation does not work properly

  #38 opened 3 years ago by axsk
  2

• Visualization of simulation results in scrolling gif

  #33 opened 3 years ago by jrdegreeff
  2