Ethanoic acid only 1 * Construct DL_POLY output files 0 * Unuse slot. opls2005 * Type of force field require (see list below for choices). kcal/mol * Energy unit: kcal/mol, kJ/mol, eV, or K. loose * Conversion criteria (strict, normal, loose) 1 * Bond type (0=default, 1=harmonic , 2=Morse) 1 * Angle type (0=default, 1=harmonic, 2=harmonic cos) none * Include user-defined information. Put 'none' or a .udff filename 1 * Verbosity mode: 1 = on, 0 = off ethanoic.mol2 * Configuration file. none * Output file in PDB. Put 'none' if not needed. 1 0.2 mol/dm^3 15.0 * Solution Maker: on/off, density, unit, cutoff) 1 * Optimise FIELD output size, if possible? 1=yes 0=no 1 * Atom display: 1 = DL_FIELD format. 2 = Standard format 2 * Vdw display format: 1 = 12-6 format 2 = LJ format default * Epsilon mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic default * Sigma mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic 1 * Epsilon mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic 2 * Sigma mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic 1 * Epsilon mixing rule (BETWEEN different FF) : 1 = geometric 2 = arithmatic 1 * Sigma mixing rule (BETWEEN different FF): 1 = geometric 2 = arithmatic 0 * Display additional info. for protein 1=Yes 0=No 0 * Freeze atoms? 1 = Yes (see below) 0 = No 0 * Tether atoms? 1 = Yes (see below) 0 = No 0 * Constrain bonds? 1 = Yes (see below) 0 = No 0 * Apply rigid body? 1 = Yes (see below) 0 = No 1 * Periodic condition ? 0=no, other number = type of box (see below) 60.0 0.0 0.0 * Cell vector a (x, y, z) 0.0 60.0 0.0 * Cell vector b (x, y, z) 0.0 0.0 60.0 * Cell vector c (x, y, z) default * 1-4 scaling for coulombic (put default or x for scaling=x) default * 1-4 scaling for vdw (put default or x for scaling=x) 0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature. 0 * Position solute at origin? 1 = yes, 0=no none 2.0 * Solvate model? none or specify solvent (see below) and distance criteria. 0 10.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute 0 * MM energy calculation. 1=Yes, 0=No 5.0 * Cut off for electrostatic energy calculation (angstrom) 5.0 * Cut off for vdw energy calculation (angstrom) ************* DL_POLY control ****************** 0 * Run DL_POLY program DLPOLY.Z * DL_POLY executable filename /home/StarPebble/Dropbox/DL_FIELD/dl_f_4.5/output * absolute path to DL_POLY program 0 * MM calculation 1=on 0=off 0 3 * Equilibration on(1)/off(0) level (1,2 or 3) 1000 * Timestep for DL_POLY runs. 9.0 * cutoff (vdw and electrostatic) 1000 * Time limit for DL_POLY run (in seconds) ######################################################## Atom state specification: type Molecular_Group filter [value] FREEZE A RIGID A TETHER CLY st 100.0 CONSTRAIN ORG1 h-bond CONSTRAIN ORG2 h-bond ######################################################### Please do not remove those '####' lines. All select atom commands must be included within the two '####' lines Available force field choices: (1) charmm Bond and Angle type: default Default 1-4 coulombic = 1.0 Default 1-4 vdw = 1.0 (2) amber Bond and Angle type: default (3) opls2005 Bond and Angle type: default (4) dreiding (general all-atom force field) Bond: harmonic or morse function Angle: harmonic or harmonic cosine function (5) pcff Bond and Angle type: default (6) charmm19 (This is united atom model) Bond and Angle type: default (7) cvff Bond and Angle type: default (8) inorganic (9) multiple Bond and Angle type: default Must specify energy unit. Must specify mixing rules BETWEEN different force fields. Select atom command summary (for FREEZE and TETHER) group_name all_backbone * For protein only. All protein backbone group_name c-alpha * For protein only. Only alpha-carbon group_name all * All atoms in group_name group_name atom_key * Atoms with the correspond key (DL_FIELD format) Select atom command summary (for CONSTRAIN) group_name h-bond * Constrain bonds with hydrogen atoms group_name all * Constrain all bonds group_name rigid_water * Fix water rigid (H-H constraints as well) Select atom command summary (for RIGID) group_name on * Apply rigid body if defined in MOLECULE (if other group_name not listed, assume rigid body is switched off) Types of solvent available: TIP3P_O - Original TIP3P TIP3P_C - TIP3P model, flexible bond (CHARMM-specific, AMBER, OPLSAA). TIP3P_E - TIP3P water model optimised for ewald sum. TIP4P - TIP4P water model (one pseudo point). TIP5P - Five-site water model (two pseudo points). TIP5P_E - Five site water model optimised for ewald sum. MeOH - Methanol, obtained from CHARMM FF IPA - Propan-2-ol, isopropyl alcohol, obtained from CHARMM FF THF - Tetrahydrofuran, obtained from CHARMM FF (please see solvent/solvent_list file for more solvent choices) Note: (1) When apply CONSTRAIN directives (either h-bond or all) to water, all bonds in water will be constrained BUT not the angle. So the water molecules are still somewhat flexible. If rigid_water is used, the H-H, in addition to O-H bonds, will be constrained. (2) If the group_name cannot be matched in the user's configuration file the select atom command will be ignored. (3) The third data column for TETHER directive is the spring constant. (4) the user-defined forcefield file (UDFF) contain BOTH user-defined structure and potential parameters information. This prevent users from tampering with the standard DL_FIELD potential library file. UDFF is where you can insert new models and new potential parameters. In addition, existing atom types and/or potential parameterscan also be redefined in UDFF file. This will OVERRIDE any existing data in the standard library files of a chosen potential scheme. The dl_field.user is an example of a user-defined forcefield file. This must be renamed as DL_FIELD.udff DO NOT use any of the examples in the file for your work. (5) If periodic image convention is NOT selected (0), then cell vectors will be ignored. Any other number indicate type of simulation box (defined as imcon in DL_POLY manual) 1 = Cubic box (D,0,0), (0,D,0), (0,0,D) 2 = Orthorhombic (D,0,0), (0,E,0), (0,0,F) 3 = Parallelepiped (La1,La2,La3), (Mb1,Mb2,Mb3),(Nc1,Mc2,Nc3) 6 = Slab (periodic in x,y but NOT z). Any other types are not available in DL_FIELD. (6) 1-4 scalings,x. For example, 1-4 Coulombic = coulombic*x (7) Epsilon and sigma mixing rule: only applicable to LJ12-6. Recommended setting is default because different FF may have different rules. (8) Solution Maker. Cutoff specifies minimum distance between molecules. Adjust this value to make molecules more spread out. If not all molecules can be fitted in a given box size, reduce the density or decrease the cutoff values. Equilibration is required (using DL_POLY) once the model is set up. Units recognised: kg/m^3, g/cm^3, mol/dm^3, molecules (9) VDW LJ 12-6 mixing rule options for epsilon and sigma: 1 = standard geometric 2 = standard arithmatic 3 = Fender-Halsey 4 = Halgren HHG For Lorentz-Berthelot rules, set epsilon = 1 and sigma = 2 For Hogervorst (good hope), set epsilon = 1 and sigma = 1 dl_field.control file: C.W. Yong, STFC, 2017.