Manual-5.0.7.Pdf

GROMACS Groningen Machine for Chemical Simulations USER MANUAL Version 5.0.7 GROMACS USER MANUAL Version 5.0.7 Contributions from Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Par¨ Bjelkmar, Rudi van Drunen, Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, Christoph Junghans, Jochen Hub, Peter Kasson, Carsten Kutzner, Brad Lambeth, Per Larsson, Justin A. Lemkul, Erik Marklund, Peiter Meulenhoff, Teemu Murtola, Szilard´ Pall,´ Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Christian Wennberg and Maarten Wolf. Mark Abraham, Berk Hess, David van der Spoel, and Erik Lindahl. c 1991–2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. c 2001–2015: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden. More information can be found on our website: www.gromacs.org. iv Preface & Disclaimer This manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is worked on continuously, which in some cases might mean the information is not entirely correct. Comments on form and content are welcome, please send them to one of the mailing lists (see www.gromacs.org), or open an issue at redmine.gromacs.org. Corrections can also be made in the GROMACS git source repository and uploaded to gerrit.gromacs.org. We release an updated version of the manual whenever we release a new version of the software, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation. On-line Resources You can find more documentation and other material at our homepage www.gromacs.org. Among other things there is an on-line reference, several GROMACS mailing lists with archives and contributed topologies/force fields. Citation information When citing this document in any scientific publication please refer to it as: M.J. Abraham, D. van der Spoel, E. Lindahl, B. Hess, and the GROMACS development team, GROMACS User Manual version 5.0.7, www.gromacs.org (2015) However, we prefer that you cite (some of) the GROMACS papers [1,2,3,4,5,6,7,8] when you publish your results. Any future development depends on academic research grants, since the package is distributed as free software! GROMACS is Free Software The entire GROMACS package is available under the GNU Lesser General Public License, version 2.1. This means it’s free as in free speech, not just that you can use it without paying us money. For details, check the COPYING file in the source code or consult http://www.gnu.org/licenses/old- licenses/lgpl-2.1.html. The GROMACS source code and and selected set of binary packages are available on our homepage, www.gromacs.org. Have fun. Contents 1 Introduction1 1.1 Computational Chemistry and Molecular Modeling................1 1.2 Molecular Dynamics Simulations..........................2 1.3 Energy Minimization and Search Methods.....................5 2 Definitions and Units7 2.1 Notation.......................................7 2.2 MD units......................................7 2.3 Reduced units....................................9 3 Algorithms 11 3.1 Introduction..................................... 11 3.2 Periodic boundary conditions............................ 11 3.2.1 Some useful box types........................... 13 3.2.2 Cut-off restrictions............................. 14 3.3 The group concept................................. 14 3.4 Molecular Dynamics................................ 15 3.4.1 Initial conditions.............................. 17 3.4.2 Neighbor searching............................. 18 3.4.3 Compute forces............................... 25 3.4.4 The leap-frog integrator.......................... 27 3.4.5 The velocity Verlet integrator....................... 27 3.4.6 Understanding reversible integrators: The Trotter decomposition..... 28 3.4.7 Twin-range cut-offs............................. 30 3.4.8 Temperature coupling........................... 31 3.4.9 Pressure coupling.............................. 37 vi Contents 3.4.10 The complete update algorithm...................... 43 3.4.11 Output step................................. 45 3.5 Shell molecular dynamics.............................. 45 3.5.1 Optimization of the shell positions..................... 45 3.6 Constraint algorithms................................ 46 3.6.1 SHAKE................................... 46 3.6.2 LINCS................................... 47 3.7 Simulated Annealing................................ 49 3.8 Stochastic Dynamics................................ 50 3.9 Brownian Dynamics................................ 51 3.10 Energy Minimization................................ 51 3.10.1 Steepest Descent.............................. 52 3.10.2 Conjugate Gradient............................. 52 3.10.3 L-BFGS................................... 52 3.11 Normal-Mode Analysis............................... 53 3.12 Free energy calculations.............................. 54 3.12.1 Slow-growth methods........................... 54 3.12.2 Thermodynamic integration........................ 56 3.13 Replica exchange.................................. 56 3.14 Essential Dynamics sampling............................ 57 3.15 Expanded Ensemble................................. 58 3.16 Parallelization.................................... 58 3.17 Domain decomposition............................... 59 3.17.1 Coordinate and force communication................... 59 3.17.2 Dynamic load balancing.......................... 59 3.17.3 Constraints in parallel........................... 60 3.17.4 Interaction ranges.............................. 61 3.17.5 Multiple-Program, Multiple-Data PME parallelization.......... 62 3.17.6 Domain decomposition flow chart..................... 64 3.18 Implicit solvation.................................. 64 4 Interaction function and force fields 67 4.1 Non-bonded interactions.............................. 67 4.1.1 The Lennard-Jones interaction....................... 68 Contents vii 4.1.2 Buckingham potential........................... 69 4.1.3 Coulomb interaction............................ 69 4.1.4 Coulomb interaction with reaction field.................. 70 4.1.5 Modified non-bonded interactions..................... 71 4.1.6 Modified short-range interactions with Ewald summation......... 72 4.2 Bonded interactions................................. 73 4.2.1 Bond stretching............................... 73 4.2.2 Morse potential bond stretching...................... 74 4.2.3 Cubic bond stretching potential...................... 75 4.2.4 FENE bond stretching potential...................... 75 4.2.5 Harmonic angle potential.......................... 76 4.2.6 Cosine based angle potential........................ 76 4.2.7 Restricted bending potential........................ 77 4.2.8 Urey-Bradley potential........................... 77 4.2.9 Bond-Bond cross term........................... 78 4.2.10 Bond-Angle cross term........................... 79 4.2.11 Quartic angle potential........................... 79 4.2.12 Improper dihedrals............................. 79 4.2.13 Proper dihedrals.............................. 80 4.2.14 Tabulated bonded interaction functions.................. 84 4.3 Restraints...................................... 85 4.3.1 Position restraints.............................. 85 4.3.2 Flat-bottomed position restraints...................... 86 4.3.3 Angle restraints............................... 87 4.3.4 Dihedral restraints............................. 87 4.3.5 Distance restraints............................. 88 4.3.6 Orientation restraints............................ 91 4.4 Polarization..................................... 95 4.4.1 Simple polarization............................. 95 4.4.2 Water polarization............................. 95 4.4.3 Thole polarization............................. 95 4.5 Free energy interactions............................... 96 4.5.1 Soft-core interactions............................ 98 4.6 Methods....................................... 100 viii Contents 4.6.1 Exclusions and 1-4 Interactions....................... 100 4.6.2 Charge Groups............................... 101 4.6.3 Treatment of Cut-offs in the group scheme................ 101 4.7 Virtual interaction sites............................... 102 4.8 Long Range Electrostatics............................. 106 4.8.1 Ewald summation.............................. 106 4.8.2 PME.................................... 107 4.8.3 P3M-AD.................................. 108 4.8.4 Optimizing Fourier transforms and PME calculations........... 108 4.9 Long Range Van der Waals interactions...................... 108 4.9.1 Dispersion correction............................ 108 4.9.2 Lennard-Jones PME............................ 110 4.10 Force field...................................... 113 4.10.1 GROMOS-96................................ 114 4.10.2 OPLS/AA.................................. 115 4.10.3 AMBER.................................. 115 4.10.4 CHARMM................................. 115 4.10.5 Coarse-grained force fields......................... 116 4.10.6 MARTINI.................................. 116 4.10.7 PLUM................................... 116 5 Topologies 117 5.1 Introduction..................................... 117 5.2 Particle type..................................... 117 5.2.1 Atom types................................. 118 5.2.2 Virtual sites................................. 118

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