1 / 28

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)

huynh
Télécharger la présentation

DL_POLY

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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)

More Related