General Information

Contributor: Jaydev Singh Rao (JaydevSR@github)

Mentor: Joe Greener (jgreener64@github)

Project: Implementation of REMD methods in JuliaMolSim/Molly.jl

https://github.com/JuliaMolSim/Molly.jl

https://github.com/JaydevSR/ReplicaExchangeMD.jl/

Major Pull Requests to Molly.jl

https://github.com/JuliaMolSim/Molly.jl/pull/86

https://github.com/JuliaMolSim/Molly.jl/pull/95

https://github.com/JuliaMolSim/Molly.jl/pull/89

https://github.com/JuliaMolSim/Molly.jl/pull/64

https://github.com/JuliaMolSim/Molly.jl/pull/76

https://github.com/JuliaMolSim/Molly.jl/pull/62

Community Bonding Period (May 20 to June 12)

• Joined the discussion in #molly channel at JuliaMolSim slack.
• Explored the documentation and features of Molly.jl
• Tried out examples available in the documentation.
• Spotted the following issues:
  • The function place_atoms did not terminate if number of atoms are more than the size of box. Fixed this using a check on maximum atoms that can fit in the box. Also added a termination conditions if an atom has not been placed after some n_attempts number of steps. PR got merged on June 4. Released in v0.10.3.
  • Spotted a bug in visualize function (due to changes in GLMakie.jl package). Fixed by chemicalfiend.
  • An bug in precompilation (Due to some conflicts with Zygote.jl), Fixed by joegreener in v0.10.3 release.

Coding Period Phase 1 (June 13 to July 25)