Read some features adn their quality from .txt files. Then it should be automatically added into LETHE

Plot the energetic landscape after having reweighed the trajectory frames with the stationary probability of the MSM

Make LETHE able to load feat in ROM instead of RAM for more usability

Compute the VAMP2 score with different features (torsion, mindist and distances) as joined plot

Make the TTClustering temperature analysis more general ie. with more than 2 temperatures

• Correct the change_submit to have :
  • Change the partition
  • Change the number of CPU per task
• Change gmx mdrun -nt $SLURM_NTASKS by $SLURM_CPUS_PER_TASK
• Add export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK before $GMX_EXE definition line
• Invert the number of tasks and the number of CPU per task
• Get more memory (64G)

Plot of the corresponding physical feat with TICA dimension.

Output representative frames taken from the PCCA++ analysis

• Concatenate the 10 trajectories in each simulation
• Compute and write the mean and the error of the concatenated result
• Obtained the drift or the deviation on the mean using gmx analyse
• Rolling average in each simulation
• Mean on the ground states

Analyze feature (two distances) and output for every trajectory for every time step in a file

Print the mean free energy of each of the meta stable state

LETHE is a application to automatize MSM analysis

Add an option to get the VAMP score of the loaded features

Plot a macrostate map without any flux, just the different state after the PCCA++ analysis

Get the eigenvalues distribution to know the number of state to use in PCCA++

Get the result of the clustering at different temperature

Concatenate all the trajectories for analysis with TTClust

Add the error coming from error on water molecules

Add the feature plot in time for checking

Add a representation of the VAMP-2 score as a function of the number of dimension to optimize the dimension reduction

Plot the VAMP-2 score as a function of the number of cluster center