{"id":4212,"date":"2017-09-11T10:13:15","date_gmt":"2017-09-11T10:13:15","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4212"},"modified":"2017-09-12T09:36:01","modified_gmt":"2017-09-12T09:36:01","slug":"v514","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/gromacs\/v514\/","title":{"rendered":"GROMACS v5.1.4"},"content":{"rendered":"

Overview<\/h2>\n

GROMACS is a package for computing molecular dynamics, simulating Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed for biochemical molecules with complicated bonded interactions (e.g. proteins, lipids, nucleic acids) but can also be used for non-biological systems (e.g. polymers).<\/p>\n\n\n
Please do not<\/strong> add the -v<\/code> flag to your mdrun<\/code> command.<\/em>
It will write to a log file every second for the duration of your job and can lead to severe overloading of the file servers.<\/td>\n<\/tr>\n<\/table>\n

Significant Change in this Version<\/h2>\n

As of Gromacs v5.1.x, the different gromacs commands (e.g., mdrun<\/code>, grompp<\/code>, g_hbond<\/code>) should now be run using the command:<\/p>\n

\r\ngmx command<\/em>\r\n<\/pre>\n
where command<\/em><\/code> is the name of the command you wish to run (without any g_<\/code> prefix), for example:<\/p>\n
\r\ngmx mdrun\r\n<\/pre>\n
The gmx<\/code> command changes its name to reflect the gromacs flavour being used but the command<\/em><\/code> does not change. For example, if using the mdrun<\/code> command:<\/p>\n
\r\n# New 5.1.4 method                     # Previous 5.0.4 method\r\ngmx   mdrun                            mdrun\r\ngmx_d mdrun                            mdrun_d\r\nmpirun -n $NSLOTS gmx_mpi   mdrun      mpirun -n $NSLOTS mdrun_mpi\r\nmpirun -n $NSLOTS gmx_mpi_d mdrun      mpirun -n $NSLOTS mdrun_mpi_d\r\n<\/pre>\n
The complete list of command<\/em><\/code> names can be found by running the following on the login node:<\/p>\n
\r\nmodule load apps\/intel-14.0\/gromacs\/5.1.4\/single\r\ngmx help commands\r\n\r\n# The following commands are available:\r\nanadock\t\t\tdyecoupl\t\tmdmat\t\tsans\r\nanaeig\t\t\tdyndom\t\t\tmdrun\t\tsasa\r\nanalyze\t\t\teditconf\t\tmindist\t\tsaxs\r\nangle\t\t\teneconv\t\t\tmk_angndx\tselect\r\nbar\t\t\tenemat\t\t\tmorph\t\tsham\r\nbundle\t\t\tenergy\t\t\tmsd\t\tsigeps\r\ncheck\t\t\tfilter\t\t\tnmeig\t\tsolvate\r\nchi\t\t\tfreevolume\t\tnmens\t\tsorient\r\ncluster\t\t\tgangle\t\t\tnmtraj\t\tspatial\r\nclustsize\t\tgenconf\t\t\torder\t\tspol\r\nconfrms\t\t\tgenion\t\t\tpairdist\ttcaf\r\nconvert-tpr\t\tgenrestr\t\tpdb2gmx\t\ttraj\r\ncovar\t\t\tgrompp\t\t\tpme_error\ttrjcat\r\ncurrent\t\t\tgyrate\t\t\tpolystat\ttrjconv\r\ndensity\t\t\th2order\t\t\tpotential\ttrjorder\r\ndensmap\t\t\thbond\t\t\tprincipal\ttune_pme\r\ndensorder\t\thelix\t\t\trama\t\tvanhove\r\ndielectric\t\thelixorient\t\trdf\t\tvelacc\r\ndipoles\t\t\thelp\t\t\trms\t\tview\r\ndisre\t\t\thydorder\t\trmsdist\t\twham\r\ndistance\t\tinsert-molecules\trmsf\t\twheel\r\ndo_dssp\t\t\tlie\t\t\trotacf\t\tx2top\r\ndos\t\t\tmake_edi\t\trotmat\t\txpm2ps\r\ndump\t\t\tmake_ndx\t\tsaltbr\r\n<\/pre>\n
Notice that the command names do NOT start with g_<\/code> and do NOT reference the flavour being run (e.g., _mpi_d<\/code>). Only the main gmx<\/code> command changes its name to reflect the flavour (see below for list of modulefiles for the full list of flavours available).<\/p>\n
To obtain more help about a particular command run:<\/p>\n
\r\ngmx help command<\/em><\/code>\r\n<\/pre>\n
For example<\/p>\n
\r\ngmx help mdrun\r\n<\/pre>\n
Helper scripts<\/h3>\n
To assist with moving to the new command calling method, we have recreated some of the individual commands that you may have used in your jobscript. For example, you can continue to use mdrun<\/code> (or mdrun_d<\/code>) instead of the new gmx mdrun<\/code> (or gmx_d mdrun<\/code>) in this release. These extra commands are automatically included in your environment when you load the gromacs modulefiles. This old method uses the flavour of gromacs in the command name (see above for comparison of new and old commands). <\/p>\n
However, please note that the following commands are new to v5.1.4 and so can only be run using the new method (gmx command<\/em><\/code>):<\/p>\n
\r\n# New commands that can only be run using: gmx command<\/em>\r\n\r\ncheck\t\t\thelp\r\nconvert-tpr\t\tinsert-molecules\r\ndistance\t\tpairdist\r\ndump\t\t\tsasa\r\nfreevolume\t\tsolvate\r\ngangle\t\t\tview\r\n<\/pre>\n
Available Flavours<\/h2>\n
This version is v5.1.4. The following flavours are available:<\/p>\n
5.1.4 for all Intel node types<\/h3>\n
Note: ability to run on all<\/em> Intel nodes implies lower optimization.<\/p>\n