Title line. Put what you want. DL_ANALYSER 2020 Energy unit kcal --- Trajectory Production Section 0 * Produce trajectory? (1=yes 0=no) t.xyz * Filename for trajectory output. (.xyz or .pdb, .mdcrd) none * PDB template (needed for .pdb trajectory output) none * Atom label to be excluded for trajectory output. Put 'none' if not require. 0 * Number of every configuration to skip 3 * 1 = Static window size, 2= dynamic window size, 3= off none * Window size (x,y,z). Put 'none' if not require. 1 5392 * Master atom index range (or put 'none') none * Atom range: start end, cut off distance, cluster shape: 1=sphere 2=cube (none to deactivate) none * Kinetic energy filter atom index range (or put 'none') none * Kinetic energy filter range, put 'none' if not require 0.0 0.0 0.0 * Translation matrix on output configuration: x, y, z (assume orthorhombic cell) --- Atom Range Definition and overall conditions for analysis as below. 1 21397 * Range of atom index (Group A). This must always define. none * Range of atom index (Group B), if applicable. Or put 'none'. 2 * Analysis type: 1=atom-based 2 = molecule-base acid 8 * Molecule-base analysis: name and no of atoms per molecule in Group A (MOLECULE A1) water 3 * Molecule-base analysis: name and no of atoms per molecule in Group A (MOLECULE A2, or 'none') none * Molecule-base analysis: name and no of atoms per molecule in Group B (MOLECULE B1, or 'none') none * For molecule-base analysis: name and no of atoms per molecule in Group B (MOLECULE B2, or 'none') all * Range of MD time (ps) samples: t1 t2 (put 'all' if all samples to be included). 0 * Assign all atoms with unit mass = 1.0 (1=yes, 0=no) 0.0 0.0 0.0 * Translation marix on coordinates:x y z (assume orthorhombic cell) auto * Periodic boundary? 0=no, other number = type of box (DLPOLY), auto = obtain from HISTORY 28.320 0.000 0.0000 * Cell vector a (x, y, z) 0.000 21.95200 0.00000 * Cell vector b (x, y, z) -2.0765488206 0.000 36.4008179166 * Cell vector c (x, y, z) 0 * Exclude any atoms for analysis? 0=no, any number = Number of EXCLUDE statements shown below. EXCLUDE 2000 to 5000 CG CGI 1 alkane 6 benzene 15 alcohol 19 ester 20 carboxylic 46 aniline 151 phosphate 800 water --- Interaction analysis (DANAI) 0 * Activate analysis (1=yes, 0=no) test.out * Output file 0 * Number of every configuration to skip 1 * Consider intra-interaction (A-A, B-B) 0 * Consider inter-interaction (A-B) 2.5 120.0 * H-bond definition: distance, angle (donor-H---acceptor) 4.5 * Hydrophobic contact distance (between alkyl carbons) 4.5 15.0 * pi-pi aromatic stacking: distance between ring, Acute angle (max.) between ring planes 0 * Cross-correlation between TWO different interactions (only works if 2 interactions are selected) 0 * alkyl-alkyl interactions (HP_1_1) 0 * aromatic-aromatic (benzene rings) interactions (HP_6_6) 0 * alcohol-alcohol (OH-OH) interactions (HB_15_15) 0 * alcohol-carboxylic interactions (HB_15_20) 0 * alcohol-aniline interactions (HB_15_46) 1 * carboxylic-carboxylic interactions (HB_20_20) 0 * carboxylic-aniline interactions (HB_20_46) 0 * water-water (HB_800_800) 0 * water-ester (HB_19_800) 0 * water-phosphate (HB_151_800) --- Structural analysis 1 * Activate analysis (1=yes 0=no) test1.out * Output file 0 * Number of every configuration to skip 0 * Block analysis (1= yes, 0=no) 0 0 * Molecular matching (1=yes, 0=no) and output option (1=yes and 0=no). none * Template file for matching (if 'none', first config in input file will be used). 0 * Center of gravity of Group, or every molecule (1=yes, 0=no) 0 * Radius of gyration (1=yes, 0=no) 0 * Asphericity (1=yes, 0=no) 0 * System density (1=yes, 0=no) 0 CTL2 CTL2 z * Chain segment orientation order parameter (1=yes, 0=no), atom_i, atom_j, director (x,y or z) 1 0.05 15.0 * Radial distribution function (RDF) (1=yes, 0 = no), bin width and cut off radius A1 A2 * Atom labels (or molecule labels) for RDF (case sensitive). Immediate bonded pair will NOT consider. 0 0.2 4.0 * Non-bonded Dihedral distribution atoms h i j k (define below), bin width, cut off between i and j OM CM CT3 OH1 * Atom labels h-i j-k for nonbonded dihedral distribution above. 0 z 0.2 60.0 all * Planar density profile (1=yes, 0=no), direction(x,y,or z), bin width, distance (+/-), label(or 'all') 0 * distance between Group A and Group B, or average distance between molecules (1=yes, 0=no) 0 * Locate maximum and minimum coordinates (1=yes, 0=no) 0 * Identify closest distance pair (1=yes, 0=no) --- Dynamical analysis 0 * Activate analysis (1=yes, 0=no) test3.out * Output file 0 * Number of every configuration to skip bulk * Surface or bulk? -1.425y 62.1y * Surface definition (top and bottom threshold) 0 * kinetic energy 1 C20 * Mean square displacement (MSD) (1=yes, 0=no). Atom label 0 100.0 * Specific heat at constant volume, temperature 0 * Center of mass velocity (1=yes, 0 = no) 0 967 * temperature (1=yes, 0=no) and constrain number, Nc. 0 13.0 * temperature profile (1=yes, 0=no) and sphere concentric radius increment 0 13.0 * velocity profile (1=yes, 0=no) and sphere concentric radius increment 0.0 -1.425 0.0 * Center point of the concentric spheres (for temperature and velocity profiles). 0 * Cross correlation displacement coefficient, C(ij) (1= yes, 2=0), some_file * File that lists atom index for cross correlation displacement coefficient --- Biological analysis (requires PDB) 0 * Activate analysis (1=yes, 0=no) bio.out * Output file 0 * Number of every configuration to skip 1 * Phi and psi dihedral, for Ramachandran plot. (1=yes, 0=no) --- Defect analysis 0 * Activate analysis (1=yes, 0=no) r.out * Output file 10 * Number of every configuration to skip surface * surface or bulk? -1.425y 62.1y * surface definition (top and bottom). 1.425 * cutoff radius around an original site. 1 * Defect distribution profile scan.(1=yes, 0=no) y * Profile direction. Scan along x, y or z direction. 0.2 * Bin width for defect distribution profiles. 1 * Defect profiles according to (1)template, or (2)current sites --- Sputter analysis 0 * Sputter analysis (1=yes, 0=no) s.out * Output file 0 * Number of every configuration to skip 0 * Detailed output (1=yes, 0=no) -47.0z 1.5z * surface definition (top and bottom surface threshold). 5.0 * surface region (thickness, centred around surface threshold) 10.0 * sputtering threshold. 4.50 * Nearest neighbour cutoff distance. --- Extract STATIS data 0 * Activate STATIS extraction? (1=yes, 0=no) statis.out * Output file 1 * system volume (stpval(19)) 0 * MD cell angle (alpha, beta, gamma) 0 * Total extended system energy 0 * Enthalpy (total energy + PV) 0 * Configurational energy 0 * Pressure (stpval(27)) 0 * System temperature 0 * Rotational temperature (stpval(11)) 0 * Core-shell temperature (stpval(20)) 0 * Core-shell potential energy (stpval(21)) 1 * Short range potential energy 0 * Electrostatic energy 0 * Chemical bond energy 0 * Valence angle and 3-body energy 0 * 4-body, dihedral and inversion energy 0 * Tethering energy 0 * Total virial 0 * short range virial 0 * Electrostatic virial 0 * Bond virial 0 * Valence and 3-body virial 0 * Constraint bond virial 0 * Tethering virial 0 * Core-shell virial 0 * PMF constrian virial (stpval(26)) ========================================================================== Note: This is DL_ANALYSER control file. DO NOT remove nor alter the headings start with '---'. Reads the following input file format (define in dl_analyser.input file): HISTORY, PDB, CONFIG, xyz, STATIS Some analysis options may not be applicable depending on the input file format and the amount of data it contains. (1) Units for length = Angstrom, temperature = Kelvin. (2) Must define at least one set of atom range (Group A) for analysis. Depending on analysis options selected, Group B atoms may be needed. (3) Analysis type: 1 = atom-base. This means analysis is carried out base on individual atoms, whenever possible. 2 = molecule-base. This means analysis is carried out base on individual molecules, whenever possible. For example, in radial distribution function, G(r), the atom-base analysis would need to define two atom labels. If molecule-base analysis is chosen, then atom labels will be ignored. Instead, the center of mass of individual molecules are determined and G(r) is calculated based on the CG values. Use Molecules A1, A2 (Group A), or B1, B2 (Group B) as labels. (3) Defect analysis can be applied for both surface and bulk models vacant - no atom around the original site. original - original atom index around the original site. new occupancy - original site is occupied by other atom index. interstitial - two or more atoms occupy a sphere around an original site. Also all other atoms that locate outside of all spheres around sites. above surface - Atoms that locate beyond the surface defintion (top and bottom). This is meaningful only for surface model. Suggested value for the cutoff RADIUS for defect analysis: NN*0.5 (NN = nearest neighbour) (4) Sputter analysis is for surface model only. adatoms - Atoms or groups of atoms that locate BEYOND the surface region that stick to the surface, determine by the NN cutoff distance measures from the surface threshold. sputtered - Atoms or groups of atoms which center of gravity pass the sputtering threshold AND, if force is available, with resultant force direct away from surface. Once it (atoms or clusters) is sputtered, it will always considered sputtered. No further analysis will be carried out. interface - particles that are located between the surface region and the sputter threshold. (5) Surface region is defined by the thickness specify, which spans along surface normal, and centred around the surface threshold (top and bottom of the threshold). -------------------------------------------- (upper limit of surface region) ^ | thickness SURFACE REGION | --------------------------------------------- (surface threshold) | SURFACE REGION V -------------------------------------------- (lower limit of surface region) (6) Sputtering threshold is the distance from the Surface definition. E.g.: If Surface definition is 1.0x and -20.0x and the Sputtering threshold is 5.0 then the real distance beyond which atoms are considered sputter is 1.0 + 5.0 and -20.0 - 5.0 in x direction. (7) Once atoms are sputtered will always considered sputter. The sputtering threshold therefore must be chosen with care as some ejected atoms may eventually fall back to the surface as adatoms or reenter surface bulk. (8) Extra information may be needed for certain calculations: Molecular matching - template file (in xyz, DL_ANALYSER format) Correlation displacement - atom index file. Just list a row of atom numbers - it indicates which atoms will be used for the calculations. (9) For C(ij) calculation - cross correlation displacement. Atom range specified above must start from 1 onwards. This is to make sure atom index match with those in input trajectory files. Only Group A atoms will be analysed. Group B, even if defined will be ignored. Any queries, requests email me: chin.yong@stfc.ac.uk --------------- DL_ANALYSER version 2.2, C W Yong, Daresbury Laboratory 2020 -----------