ravenswing/mdsaps

Molecular Dynamics - Simulation Analysis and Preparation Suite

mdsaps's Issues

[tools] Combine COM Dist Functions with Dist

• Combine com_dist_per_frame and dist_per_frame
• Combine measure_com_dist and measure_dist
• Combine save_com_dist and save_dist

[plot] Multiplots

• Add axis input and/or output to existing plotting
• Make multiplot function
• Test multiplot function

Reweighting

• Work out the best method for reweighting
• Implement reweighting in 1D
• Add to convergence sumhills and/or plots
• Implement reweighting in 2D
• Test reweighting
• [EXTRA] Add parallelisation for reweighting

[load] [plolt] Fun-metaD FES

• Make sure load.fes works with fun-metaD FES
• Make sure plot.fes2D works with fun-metaD FES

[lib] Add to all files to lib

ALL external scripts that are copied or used:

• PLUMED template files
• local_dirs .sh & .mdp files for system prep.
• GMX forcefields

[sys prep] Gromacs Improvements

• unify running with apo vs. holo
• make sure naming and argument ordering is consistent
• better group selection (e.g. Protein_LIG throughout)
• --> auto-renaming Protein -> Protein_LIG in .mdp and .sh files
• new function: auto-run prep
• fix: fix_itp_includes interaction with chains and numbers
• fix: step 04 POSRES Ca renaming
• ??? put input files into lib
• [EXTRA] create a pipeline for more automatic running over many systems

Documentation

• Update base README.
• Find the best way to document/auto-document the code.
• [EXTRA] Add buttons/images to README.

Standardise variable names

Ensure that the ordering and name of input variables are consistent

• traj_path
• top_path
• out_path
• select
  etc...