Simulator

  • In PaCS-MD, simulations corresponding to the simulator are executed. Gromacs, Amber, and NAMD are supported.
  • In each cycle, n_replica simulations are executed. n_parallel simulations are will run in parallel. If n_replica is not a multiple of n_parallel, or in cycle 0, the remainder of the simulations will run in series.
  • If you want to run multiple replica simulations in parallel using MPI, set cmd_mpi. If cmd_mpi is not set, parallel execution will be performed using the multiprocessing module of python.

Content

When are cmd_serial & cmd_parallel used ?

  • See the table below for cmd_serial and cmd_parallel in the input file. cmd_serial is used if cycle0 or n_parallel=1. If n_replica is not divisible by n_parallel, then cmd_serial is used for the remaining replicas. Otherwise, cmd_parallel is used.
GPUMPIn_parallelcommand
xx1cmd_serial
xxncmd_serial
xo1cmd_serial
xoncmd_parallel
ox1cmd_serial
oxncmd_serial
oo1cmd_seiral
ooncmd_parallel

Gromacs

To run the simulation using gromacs, write in the inputfile as in this example. The details of each keyword are as follows.

keywords

  • simulator: str, required
    • Software used inside PaCS-MD. e.g. "gromacs"
  • cmd_mpi: str, default=""
    • Command for MPI parallelizataion. e.g. "mpirun -np 4"
  • cmd_serial: str, required
    • Command to run simulation in serial. e.g. "gmx_mpi mdrun -ntomp 6"
  • cmd_parallel: str, default=cmd_serial
    • Command to run simulation in parallel. e.g. "gmx_mpi mdrun -ntomp 6"
  • structure: str, required
    • Structure file path for MD simulation. e.g. "./input.gro"
    • This is also used as the initial structure of PaCS-MD
  • topology: str, required
    • Topology file path for MD simulation. e.g. "./topol.top"
  • mdconf: str, required
    • Parameter file path for MD simulation. e.g. "./parameter.mdp"
  • index_file: str, required
    • Gromacs index file path. e.g. "./index.ndx"
  • trajectory_extension: str, required
    • Trajectory file extension. (The "." is necessary.) e.g. ".trr"

Amber

To run the simulation using amber, write in the inputfile as in this example. The details of each keyword are as follows.

keywords

  • simulator: str, required
    • Software used inside PaCS-MD. e.g. "amber"
  • cmd_mpi: str, default=""
    • Command for MPI such as mpirun. e.g. "mpirun -np 4"
  • cmd_serial: str, required
    • Command to run simulation in serial. e.g. "pmemd.cuda"
  • cmd_parallel: str, default=cmd_serial
    • Command to run simulation in parallel. e.g. "pmemd.cuda"
  • structure: str, required
    • Structure file path for MD simulation. e.g. "./input.rst7"
    • This is also used as the initial structure of PaCS-MD.
  • topology: str, required
    • Topology file path for MD simulation. e.g. "./topology.parm7"
  • mdconf: str, required
    • Parameter file path for MD simulation. e.g. "./parameter.mdin"
  • trajectory_extension: str, required
    • Trajectory file extension. (The "." is necessary.) e.g. ".nc"

NAMD

To run the simulation using NAMD, write in the inputfile as in this example. The details of each keyword are as follows.

keywords

  • simulator: str, required
    • Software used inside PaCS-MD. e.g. "namd"
  • cmd_mpi: str, default=""
    • Command for MPI parallelizataion. e.g. "mpirun -np 4"
  • cmd_serial: str, required
    • Command to run simulation in serial. e.g. "namd2 +p4"
  • cmd_parallel: str, default=cmd_serial
    • Command to run simulation in parallel. e.g. "namd2 +p4"
  • structure: str, required
    • Structure file path for MD simulation. e.g. "./input.pdb"
    • This is also used as the initial structure of PaCS-MD.
  • topology: str, required
    • Topology file path for MD simulation. e.g. "./topology.psf"
  • mdconf: str, required
    • Parameter file path for MD simulation. e.g. "./parameter.conf"
  • trajectory_extension: str, required
    • Trajectory file extension. (The "." is necessary.) e.g. ".dcd"