bwGRID

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CPMD.org

What is Gromacs?

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:

URL: Gromacs.org

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen, now maintained and extended at different places, including the University of Uppsala, University of Stockholm and the Max Planck Institute for Polymer Research. GROMACS is open source software released under the GPL.

 

  • The actual distribution of Gromacs we are running is: 4.5.5

    Installed programs (in /opt/bwgrid/chem/gromacs/4.5.5_(xxxx)-openmpi-1.4.3-intel-12.0/bin):

    completion.bash  g_densorder  g_sorient   g_energy   g_order      g_anaeig   g_densmap      xpm2ps     g_luck
    completion.csh   g_hydorder   g_spatial   g_filter   g_polystat   g_analyze  g_dielectric   do_dssp    gmxcheck
    completion.zsh   g_kinetics   g_spol      g_gyrate   g_potential  g_angle    g_dih          editconf   gmxdump
    demux.pl         g_mdmat      g_tcaf      g_h2order  g_rama       g_bar      g_dipoles      eneconv    g_protonate
    GMXRC            g_membed     g_traj      g_hbond    g_rdf        g_bond     g_disre        genbox     g_x2top
    GMXRC.bash       g_options    g_tune_pme  g_helix    g_rms        g_bundle   g_dos          genconf    grompp
    GMXRC.csh        g_pme_error  g_vanhove   g_lie      g_rmsdist    g_chi      genion         genrestr   mdrun
    GMXRC.zsh        g_sas        g_velacc    g_mindist  g_rmsf       g_cluster  g_helixorient  g_nmtraj   pdb2gmx
    g_xrama          g_select     g_wham      g_morph    g_rotacf     g_confrms  g_principal    make_ndx   tpbconv
    ngmx             g_sgangle    g_dist      g_msd      g_rotmat     g_covar    g_wheel        mk_angndx
    xplor2gmx.pl     g_sham       g_dyndom    g_nmeig    g_saltbr     g_current  make_edi       trjcat
    g_clustsize      g_sigeps     g_enemat    g_nmens    g_anadock    g_density  trjorder       trjconv

bwGRID Anpassungen / adaptations

bwGRID-Setups

Main Programm (Gromacs Single Precision)

These are setups for the SINGLE-PRECISION version only!

WARNING: do not use the gcc 4.1.x set of compilers. They are broken.

Description: Module - File
Path/Filename: /opt/bwgrid/chem/gromacs/4.5.5_single-openmpi-1.4.3-intel-12.0/modulefiles/chem-gromacs-4.5.5_single-openmpi-1.4.3-intel-12.0

bwGRID examples

The PBS batch system can be used to manage the nodes allocation in a cluster of hosts. For example, using a particular job script, it's possible to communicate to the MPI launcher program (mpirun) the number and the list of nodes that PBS has allocated for the whole job as requested from the user. The PBS server will not run more jobs on the busy nodes until the end of the current job. Here is an example of a script to do this over our bwGRID network using an implementation of Open-MPI.

All-In-One: bwGRID - Example PBS and Data File for submitting a job via. 'qsub'
Path/Filename: /opt/bwgrid/chem/gromacs/4.5.5_single-openmpi-1.4.3-intel-12.0/bwgrid-examples/gromacs-4.5.5_single-bwgrid-examples.tgz
Description: bwGRID - PBS-file only
Path/Filename: /opt/bwgrid/chem/gromacs/4.5.5_single-openmpi-1.4.3-intel-12.0/bwgrid-examples/gromacs-4.5.5_single-bwgrid-examples.pbs

© Gromacs is copyrighted by General Public License (GPL). It's completely free.
Δ 11.01.2012 | initial version | rainer.rutka(at)uni-konstanz.de