DL_POLY Miguel A. Gonzalez Institut Laue-Langevin

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Presentation transcript:

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) 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 DL_POLY force field

DL_POLY force field: Bond potentials 4 DL_POLY force field: Bond potentials

DL_POLY force field: Van der Waals potentials 5 DL_POLY force field: Van der Waals potentials

DL_POLY force field Intramolecular forces: 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)

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.

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

DL_POLY input/output files

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):

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

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

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

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

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)

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

DL_POLY output: RDFDAT Optional ASCII file containing partial RDFs

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)

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

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

The DL_POLY Java GUI FileMaker

The DL_POLY Java GUI FileMaker

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

The DL_POLY Java GUI Analysis

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

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

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 …

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)