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Manual-2020.Pdf GROMACS Documentation Release 2020 GROMACS development team Jan 01, 2020 CONTENTS 1 Downloads 2 1.1 Source code.............................................2 1.2 Regression tests...........................................2 2 Installation guide 3 2.1 Introduction to building GROMACS................................3 2.1.1 Quick and dirty installation.................................3 2.1.2 Quick and dirty cluster installation.............................3 2.1.3 Typical installation.....................................4 2.1.4 Building older versions...................................4 2.2 Prerequisites.............................................4 2.2.1 Platform...........................................4 2.2.2 Compiler..........................................4 2.2.3 Compiling with parallelization options...........................5 2.2.4 CMake...........................................6 2.2.5 Fast Fourier Transform library...............................6 2.2.6 Other optional build components..............................8 2.3 Doing a build of GROMACS....................................8 2.3.1 Configuring with CMake..................................8 2.3.2 Compiling and linking................................... 15 2.3.3 Installing GROMACS.................................... 15 2.3.4 Getting access to GROMACS after installation...................... 16 2.3.5 Testing GROMACS for correctness............................ 16 2.3.6 Testing GROMACS for performance............................ 17 2.3.7 Validating GROMACS for source code modifications................... 17 2.3.8 Having difficulty?...................................... 18 2.4 Special instructions for some platforms............................... 18 2.4.1 Building on Windows.................................... 18 2.4.2 Building on Cray...................................... 19 2.4.3 Building on Solaris..................................... 19 2.4.4 Fujitsu PRIMEHPC..................................... 19 2.4.5 Intel Xeon Phi........................................ 19 2.5 Tested platforms........................................... 20 3 User guide 21 3.1 Getting started............................................ 21 3.1.1 Flow Chart......................................... 21 3.1.2 Setting up your environment................................ 23 3.1.3 Flowchart of typical simulation............................... 23 3.1.4 Important files........................................ 23 3.1.5 Tutorial material...................................... 25 3.1.6 Background reading..................................... 25 3.2 System preparation.......................................... 25 3.2.1 Steps to consider...................................... 25 i 3.2.2 Tips and tricks....................................... 26 3.3 Managing long simulations..................................... 27 3.3.1 Appending to output files.................................. 27 3.3.2 Backing up your files.................................... 28 3.3.3 Extending a .tpr file..................................... 28 3.3.4 Changing mdp options for a restart............................. 28 3.3.5 Restarts without checkpoint files.............................. 28 3.3.6 Are continuations exact?.................................. 28 3.3.7 Reproducibility....................................... 29 3.4 Answers to frequently asked questions (FAQs)........................... 30 3.4.1 Questions regarding GROMACS installation........................ 30 3.4.2 Questions concerning system preparation and preprocessing............... 30 3.4.3 Questions regarding simulation methodology....................... 31 3.4.4 Parameterization and Force Fields............................. 31 3.4.5 Analysis and Visualization................................. 32 3.5 Force fields in GROMACS...................................... 32 3.5.1 AMBER........................................... 32 3.5.2 CHARMM......................................... 33 3.5.3 GROMOS.......................................... 34 3.5.4 OPLS............................................ 34 3.6 Command-line reference....................................... 34 3.6.1 molecular dynamics simulation suite............................ 34 3.6.2 gmx anaeig......................................... 39 3.6.3 gmx analyze......................................... 41 3.6.4 gmx angle.......................................... 44 3.6.5 gmx awh.......................................... 46 3.6.6 gmx bar........................................... 46 3.6.7 gmx bundle......................................... 48 3.6.8 gmx check.......................................... 50 3.6.9 gmx chi........................................... 51 3.6.10 gmx cluster......................................... 54 3.6.11 gmx clustsize........................................ 56 3.6.12 gmx confrms........................................ 58 3.6.13 gmx convert-tpr....................................... 59 3.6.14 gmx convert-trj....................................... 59 3.6.15 gmx covar.......................................... 61 3.6.16 gmx current......................................... 62 3.6.17 gmx density......................................... 64 3.6.18 gmx densmap........................................ 65 3.6.19 gmx densorder....................................... 67 3.6.20 gmx dielectric........................................ 68 3.6.21 gmx dipoles......................................... 69 3.6.22 gmx disre.......................................... 71 3.6.23 gmx distance........................................ 73 3.6.24 gmx do_dssp........................................ 74 3.6.25 gmx dos........................................... 75 3.6.26 gmx dump.......................................... 77 3.6.27 gmx dyecoupl........................................ 78 3.6.28 gmx editconf........................................ 79 3.6.29 gmx eneconv........................................ 81 3.6.30 gmx enemat......................................... 82 3.6.31 gmx energy......................................... 83 3.6.32 gmx extract-cluster..................................... 86 3.6.33 gmx filter.......................................... 87 3.6.34 gmx freevolume....................................... 88 3.6.35 gmx gangle......................................... 90 3.6.36 gmx genconf........................................ 91 3.6.37 gmx genion......................................... 92 ii 3.6.38 gmx genrestr........................................ 93 3.6.39 gmx grompp......................................... 94 3.6.40 gmx gyrate......................................... 97 3.6.41 gmx h2order......................................... 98 3.6.42 gmx hbond......................................... 99 3.6.43 gmx helix.......................................... 101 3.6.44 gmx helixorient....................................... 103 3.6.45 gmx help.......................................... 104 3.6.46 gmx hydorder........................................ 104 3.6.47 gmx insert-molecules.................................... 105 3.6.48 gmx lie........................................... 106 3.6.49 gmx make_edi....................................... 107 3.6.50 gmx make_ndx....................................... 110 3.6.51 gmx mdmat......................................... 111 3.6.52 gmx mdrun......................................... 112 3.6.53 gmx mindist......................................... 116 3.6.54 gmx mk_angndx...................................... 117 3.6.55 gmx msd.......................................... 118 3.6.56 gmx nmeig......................................... 119 3.6.57 gmx nmens......................................... 121 3.6.58 gmx nmr........................................... 121 3.6.59 gmx nmtraj......................................... 123 3.6.60 gmx nonbonded-benchmark................................ 123 3.6.61 gmx order.......................................... 125 3.6.62 gmx pairdist......................................... 126 3.6.63 gmx pdb2gmx........................................ 128 3.6.64 gmx pme_error....................................... 131 3.6.65 gmx polystat........................................ 131 3.6.66 gmx potential........................................ 132 3.6.67 gmx principal........................................ 134 3.6.68 gmx rama.......................................... 134 3.6.69 gmx rdf........................................... 135 3.6.70 gmx report-methods..................................... 137 3.6.71 gmx rms........................................... 137 3.6.72 gmx rmsdist......................................... 139 3.6.73 gmx rmsf.......................................... 140 3.6.74 gmx rotacf.......................................... 142 3.6.75 gmx rotmat......................................... 143 3.6.76 gmx saltbr.......................................... 144 3.6.77 gmx sans.......................................... 144 3.6.78 gmx sasa.......................................... 146 3.6.79 gmx saxs.......................................... 147 3.6.80 gmx select.......................................... 148 3.6.81 gmx sham.......................................... 150 3.6.82 gmx sigeps......................................... 152 3.6.83 gmx solvate......................................... 153 3.6.84 gmx sorient......................................... 154 3.6.85 gmx spatial......................................... 155 3.6.86 gmx spol.......................................... 157 3.6.87 gmx tcaf..........................................
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