Overview

generated files

• mdrun reads the file specified by -f and performs MD calculations according to its contents.
• After the command is executed, the following directory structure is created.

• The directory structure is created as shown above, and the following files are created.
  • trajectory file
    • The trajectory file is a file that contains the coordinates of the atoms in the system at each time step.
    • file name without extension is prd and the extension is determined by the input file.
  • cv.log
    • The cv.log file contains the calculated collective variable (CV) values for each frame in the trajectory file.
    • first column: replica number (1-indexed)
    • second column: frame number (1-indexed)
    • third column: CV value
  • cv_ranked.log
    • The cv_ranked.log file contains the sorted CV values.
  • progress.log
    • The progress.log file contains the progress of the simulation in each cycle.

Overall diagram

• PaCS-MD runs multiple short simulations, from which it selects a snapshot that meets its objectives and serves as the initial structure for the next cycle. Therefore, the diagram is as follows.

sequenceDiagram

participant cycle as cycle
participant simulator as simulator
participant analyzer as analyzer
loop 0, max_cycle
    Note over cycle: prepare initial structures
    par run short MD simulations
    cycle ->>+ simulator: run short MD simulations
    simulator ->>- cycle: trajectory files
    end
    par calculate CV 
    cycle ->>+ analyzer: calculate CV
    Note over analyzer: calculate CV based on the input file.
    Note over analyzer: sort the snapshots based on the CV.
    analyzer ->>- cycle: cv.log, cv_ranked.log
    end
    break the top CV reaches threshold
    analyzer -->> cycle: finish PaCS-MD
    end
    Note over cycle: export top N snapshots to next cycle.
end

• simulator

  • The simulator performs one short MD on the starting structure in cycle 0.
  • In the other cycles, it executes n_replica short MDs, starting from the top-ranking structure of each cycle.
  • Currently, only GROMACS, AMBER and NAMD are supported.
  • See Simulator for more information

• analyzer

  • The analyzer calculates the collective variable (CV) based on the type specified in the input file.
  • The analyzer sorts the structures in each trajectory based on the CV.
  • User-defined types are also available.
  • See Analyzer for more information