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MACSIMUS Manual 1 MACSIMUS manual benzocaine (ethylaminobenzoate) parameter_set = charmm21 HA | HA-CT-HA | HA-CT-HA | OSn.2 | Cp.7=On.5 | C6R--C6R-HA Most often used links: | | HA-C6R C6R-HA 2.2 Blend synopsis and options | | HA-C6R--C6R-NPn.5^-Hp.25 9.2 Cook synopsis and options | 9.2.5 Cook input data Hp.25 MACromolecule SIMUlation Software © Jiˇr´ıKolafa 1993{2020 MACSIMUS may be distributed under the terms of the GNU General Public Licence Credits: ray: Mark VandeWettering \reasonably intelligent raytracer" CHARMM force field (files: charmm*.par, charmm*/*.rsd) GROMOS force field (files: gromos*.par, gromos*/*.rsd) amoeba implementation by Z. Wagner moil support by J. Schofield several bug fixes by T. Trnka bug discovered by N. Parfenov Contents I Program `blend' version 2.4b 14 1 Introduction 16 1.1 Force fields...................................... 16 1.2 `blend' overview.................................... 16 1.3 Versions........................................ 17 2 Running blend 18 2.1 Environment...................................... 18 2.2 Synopsis........................................ 19 2.2.1 Global options................................. 19 2.2.2 par-options and parameter files....................... 20 2.2.3 mol-options and molecular files....................... 22 2.2.4 Extra-options ................................. 29 2.3 File extensions.................................... 34 2.4 Run-time control................................... 37 2.4.1 get data format for input........................... 37 2.4.2 Scrolling.................................... 38 2.4.3 Error handling................................ 39 2.4.4 Interrupts................................... 40 2.5 Showing molecules graphically............................ 40 2.5.1 X11 Graphics................................. 40 2.5.2 Playback output............................... 44 2.6 Energy minimization................................. 44 2.7 Missing coordinates.................................. 45 3 Force field and the parameter file 46 3.1 Structure of the parameter file............................ 46 3.2 Force field generation options............................ 46 3.3 Table of atoms.................................... 49 2 3 3.4 Non-bonded forces.................................. 50 3.4.1 Selection of site{site and Coulomb energy terms.............. 51 3.4.2 Combining rules for the Lennard-Jones parameters............ 51 3.4.3 Table of site{site parameters......................... 52 3.4.4 Non-bonded fixes............................... 53 3.4.5 Table of polar atom parameters....................... 53 3.4.6 Table \shellrep" of repulsive counterparts.................. 54 3.4.7 Table of axially polar bonds......................... 54 3.4.8 Table of 1{3 axially polar groups...................... 55 3.4.9 Table defining water models......................... 55 3.4.10 Table defining the protein backbone types................. 57 3.5 Non-bonded potential cutoff............................. 58 3.6 Bond potential.................................... 58 3.7 Bond angle potential................................. 59 3.8 Torsions........................................ 60 3.8.1 Torsion angle................................. 60 3.8.2 Torsion potential............................... 60 3.8.3 Conversion of dihedrals............................ 61 3.8.4 Cis and trans-dihedrals............................ 62 3.8.5 Implementation of the torsion potential................... 63 3.8.6 Chirality.................................... 63 3.8.7 Dihedrals in aromatic rings......................... 64 3.8.8 Tables of dihedrals and impropers...................... 64 3.8.9 Atom matching rules for finding the energy terms............. 65 4 Description of molecules 66 4.1 Molecular file (mol-file) format............................ 66 4.2 Chemical file format................................. 67 5 Output format (ble-file) 70 5.1 Global parameters.................................. 70 5.2 Site types....................................... 72 5.3 Non-bonded fixes................................... 72 5.4 Header of molecule.................................. 73 5.5 One species (molecule) data............................. 73 5.6 Table of sites..................................... 74 5.7 Tables of bonds and bond angles.......................... 75 4 5.8 Tables of dihedrals, impropers and aromatics.................... 76 5.9 Table of axial polarizability tensors......................... 77 5.10 Table of dependants................................. 77 5.10.1 Lone (out-of-plane) dependants....................... 78 6 Examples 80 6.1 Example 1: Protein in water............................. 80 6.2 Example 2: Cluster Na4Cl4............................. 81 6.3 Crystals........................................ 82 7 Problems 85 7.1 Bugs and caveats................................... 85 7.2 Trouble shooting................................... 85 7.3 Frequently asked questions.............................. 87 7.3.1 Free molecules................................. 87 7.3.2 Prevent molecules from evaporating..................... 88 7.3.3 One or more molecules?........................... 88 II Program `cook' version V3.4h 89 8 Overview 91 8.1 Features of cook ................................... 91 8.2 History......................................... 92 8.3 Compile-time versions of cook ............................ 93 8.4 Disclaimer....................................... 95 9 Running cook 96 9.1 Where is........................................ 96 9.2 Synopsis........................................ 96 9.2.1 File parameters................................ 96 9.2.2 Options.................................... 97 9.2.3 File extensions................................ 103 9.2.4 Program flow................................. 109 9.2.5 Input data................................... 109 9.2.6 Interactive and batch control........................ 145 9.2.7 Interrupt.................................... 146 10 Parallelization 147 5 10.1 Compiling....................................... 147 10.2 Running........................................ 147 10.3 Linked-cell list and Ewald parallelized........................ 147 10.4 Ewald k-space and r-space running in parallel................... 148 10.5 Pair sums for a single big molecule parallelized................... 148 11 Algorithms and parameters 149 11.1 Accuracy........................................ 149 11.1.1 Errors of constraints............................. 150 11.1.2 Energy conservation............................. 150 11.1.3 Self-consistent field accuracy......................... 151 11.2 How to set Ewald parameters α and κ ....................... 151 11.2.1 Simple way.................................. 152 11.2.2 More accurate way.............................. 152 11.2.3 Most accurate way.............................. 152 11.3 Constraint dynamics................................. 154 11.3.1 The SHAKE algorithm with Verlet integration............... 154 11.3.2 Constraint dynamics with Gear integrators................. 155 11.3.3 Constraint forces by Lagrange multipliers.................. 156 11.3.4 Correcting constraints............................ 156 11.3.5 Dependants.................................. 157 11.4 Site{site potential cutoff............................... 160 11.5 The timestep..................................... 161 11.6 Functions for r-space Ewald sums.......................... 162 12 NVT and NPT ensembles 163 12.1 Kinetic temperature................................. 163 12.1.1 Should we subtract 1 from nf for energy conservation?.......... 163 12.2 Constant temperature simulations.......................... 165 12.2.1 The Berendsen (friction) thermostat.................... 165 12.2.2 Decoupled translational and intramolecular thermostats.......... 166 12.2.3 The Nos´e{Hoover canonical ensemble.................... 166 12.2.4 Maxwell{Boltzmann thermostat....................... 167 12.2.5 Langevin thermostat............................. 168 12.2.6 Which thermostat............................... 168 12.3 Constant pressure simulations............................ 168 12.3.1 Friction (Berendsen) barostats........................ 169 6 12.3.2 MTK thermostat and barostat........................ 169 12.3.3 Simulation along given V (t) time dependence............... 172 12.3.4 Adjusting force field parameter to pressure................. 172 13 Initial configuration 174 13.1 Random-shooting algorithm............................. 174 13.2 Crystal initial configuration............................. 175 13.3 Immersing a large solute into solvent........................ 175 14 Measurements 177 14.1 Units of measurements................................ 177 14.2 Convergence profile.................................. 177 14.3 Analysis of statistical errors............................. 178 14.4 Kinetic quantities from equilibrium molecular dynamics.............. 180 14.4.1 Diffusivity................................... 180 14.4.2 Conductivity................................. 181 14.4.3 Viscosity.................................... 182 14.5 Kinetic quantities from the Einstein relations.................... 183 14.5.1 Requirements................................. 183 14.5.2 Usage..................................... 183 14.5.3 Results..................................... 184 14.5.4 Analysis of results.............................. 185 14.6 Structure factor.................................... 186 14.6.1 Structure factor for pure simple fluids.................... 186 14.6.2 Structure factor for mixtures........................
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