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DL_POLY

DL_POLY. Miguel A. Gonzalez Institut Laue-Langevin (Based on http://www.ccp5.ac.uk/DL_POLY/TUTORIAL/). The DL_POLY Molecular Simulation Package. General purpose classical MD From Daresbury Lab., started in 1994 (Smith, Forester and Todorov)

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DL_POLY

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  1. DL_POLY Miguel A. Gonzalez Institut Laue-Langevin (Based on http://www.ccp5.ac.uk/DL_POLY/TUTORIAL/)

  2. The DL_POLY Molecular Simulation Package • General purpose classical MD • From Daresbury Lab., started in 1994 (Smith, Forester and Todorov) • Fortran 90 code to compile (no executables distributed) • Former version  DL_POLY_CLASSIC (CCPForge under BSD license) • Supported version  DL_POLY_4 (STFC licence, free to academic) • Designed for UNIX/Linux (but can run on a Windows PC with CygWin) • Choice between DL_POLY_CLASSIC and DL_POLY_4: • DL_POLY_CLASSIC if <30,000 atoms, <100 procs • DL_POLY_CLASSIC if metadynamics, hyperdynamics needed • DL_POLY_4 if >105 atoms, ~103 procs • Limited GUI and user utilities, but: • Java GUI • DL_POLY_FIELD • Fortran analysis utilities

  3. 3 DL_POLY force field

  4. 4 DL_POLY force field: Bond potentials

  5. 5 DL_POLY force field: Van der Waals potentials

  6. 6 DL_POLY force field • Intramolecular forces: • Bonds, angle, dihedrals, inversions • Intermolecular forces: • All common van der Waals potentials • Sutton Chen approximate many-body potential (for metals) • 3-body angle forces (e.g. silicates) • 4-body inversion forces (e.g. borates) • Tabulated potential • Coulombic: • - Reaction field, Ewald, SPME, HKE (for 2D systems), dynamical and relaxed shell models (for polarizable systems)

  7. DL_POLY algorithms and ensembles • Verlet (leapfrog and velocity) • SHAKE and RATTLE (for bond constraints) • Quaternions (for rigid units) • NVE • NVT (Nose-Hoover, Berendsen and Gaussian constraints) • NPT (Hoover and Berendsen) with cell size variation only or size+shape • Multiple timestep • Different boundary conditions available: None, orthorhombic, parallelepiped, truncated octahedral, rhombic dodecahedral, slabs.

  8. DL_POLY structure build Makefiles source Source code execute Executable & working directory DL_POLY java Java GUI source code utility Utility codes data Test data

  9. DL_POLY input/output files

  10. DL_POLY input: CONFIG Give size of simulation box, key for PBC and list of atoms and coordinates (possible to include also velocities and forces):

  11. DL_POLY input: FIELD Full description of force field (including all possible intramolecular interactions):

  12. DL_POLY input: CONTROL Commands to run the simulation: Temperature, pressure, ensemble, integrator, cutoffs, number of steps, etc.

  13. DL_POLY output: OUTPUT ASCII file containing a summary of the simulation:

  14. DL_POLY output: OUTPUT ASCII file containing a summary of the simulation:

  15. DL_POLY output: STATIS ASCII file containing system properties (T, P, energies, etc.) at selected intervals. Intended for statistical analysis and plotting (e.g. using Java GUI)

  16. DL_POLY output: REVCON Similar to CONFIG, contains the final configuration of the simulation run

  17. DL_POLY output: RDFDAT Optional ASCII file containing partial RDFs

  18. DL_POLY output: HISTORY • ASCII file containing the trajectory at selected intervals. • For each configuration contains: • Time step and data keys • Cell matrix • Atom name, index, mass and charge • Positions • Velocities and forces (optional)

  19. DL_POLY output: REVIVE Binary file containing all the necessary information to continue or restart a simulation: - Copy/Move REVIVE to REVOLD - Copy/Move REVCON to CONFIG - Use restart keyword in CONTROL

  20. The DL_POLY Java GUI java – jar ../java/GUI.jar

  21. The DL_POLY Java GUI FileMaker

  22. The DL_POLY Java GUI FileMaker

  23. The DL_POLY Java GUI FileMaker OK if a single type of molecule Dreiding/OPLS included (?)

  24. The DL_POLY Java GUI Analysis

  25. DL_POLY input builder: DL_FIELD Support utility to create the input files needed for DL_POLY Created by C. W. Yong (STFC Daresbury Lab.) on 2010 C code to compile Aim: Atomic configuration  CONFIG + FIELD + CONTROL CHARMM Several water models AMBER OPLS-AA

  26. DL_POLY visualization • Some programs allow loading directly the HISTORY file in order to make a movie of the trajectory or apply some analysis: • nMoldyn • VMD • gOpenMol

  27. DL_POLY examples of use W. Smith et al., Mol. Simul. 28, 385-471 (2002) W. Smith (Guest Editor), Mol. Simul. 32, 933-1121 (2006) • Liquids and solutions • Ionic solids • Molecular crystals • Liquid crystals • Polymers • Membranes • …

  28. DL_POLY exercises http://www.ccp5.ac.uk/DL_POLY/TUTORIAL/EXERCISES/index.html • Phase transition in KCl using anisotropic constant pressure MD • Fast ion conduction in AgI • K+ capture by valinomycin in vacuo • Water using different algorithms • Potential of Mean Force for H2O-K+ • Diffusion of benzene in a zeolite • Structure and dynamics of liquid Ar • A carbon nanoswitch • Absorption of formic acid onto a calcite surface • Or try other test data included in the distribution • Or try your own system (e.g. using a PDB configuration file + DL_FIELD)

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