Tutorial

Molecular dynamics simulation of DHFR

DHFR (dihydrofolate reductase) is a protein commonly used as a benchmark in MD simulations.

For the simulation, you need:

  • Prepare the simulation system and corresponding force field files
  • Write ACEMD3 input file
  • Run the simulation with ACEMD3

All these tasks can be done easily with HTMD: follow the tutorial of the molecular dynamics protocols.

Alternatively, you can run the simulation with ACEMD3 directly:

  • Download already prepared files for the DHFR simulation with CHARMM 22 force field:

  • An input options for NVT (298.15 K) simulation:

    parameters par_all22_prot.prm
    structure dhfr.psf
    
    coordinates dhfr.pdb
    celldimensions 62.23 62.23 62.23
    temperature 298.15
    
    thermostat on
    thermostatTemp 298.15
    
    run  100ns
    

    Save it to an input file. By default, ACEMD3 uses 4 fs time step and applies necessary constraints automatically. The other simulation parameters are set the standard values (see the input file options for details).

  • Start the simulation:

    $ acemd3 input
    

    By default, ACEMD3 runs on the first GPU (device 0). This can be changed with --device argument (see the command line arguments for details). Note that ACEMD Pro licence is required to run on all GPUs.

    During the course of the simulation, log messages are written to the standard output and simulation trajectory is saved to output.xtc. Also, the simulation state is periodically saved to restart.chk (see the input options for details).

Migrating from the old ACEMD

ACEMD3 is a substantial development over the previous version (i.e. ACEMD). The main changes affecting users:

  • Simplified input file
  • Discontinued TCL scripting

If you are using ACEMD via HTMD, the migration is trivial: just check ACEMD module for instructions.

If you are using ACEMD directly, the migration needs some work:

  • Some input options have to been removed or changed (see the input options for details). Note that ACEMD3 accepts some old options, but prints warning messages.
  • Discontinued TCL scripts have to replaced with the restraint options (see the restrain options for details).