Gromacs 4.6.1

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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:

GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or Fortran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for i386 processors, separate versions using all x86-64 registers are used on Opteron x86-64 and Xeon EM64t machines. This results in exceptional performance on inexpensive PC workstations, and for Pentium IV/Opteron processors there are also SSE2 double precision assembly loops. There are new manually tuned assembly loops for ia64 (both single and double precision), and last but certainly not least we have written Altivec assembly loops both for Linux and Mac OS X. Gromacs is normally 3-10 timesfaster than any other program; check the article in Journal of Molecular Modeling (reference can be found under resources) for a comparison benchmark.

GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading.

There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs.

As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished.

Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision.

GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.

GROMACS comes with a large selection of flexible tools for trajectory analysis - you won`t have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!

A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.

GROMACS can be run in parallel, using standard MPI communication.

GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.

The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.

There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.

Software OS: Windows XP/2003/2008

Distribution:Open source

Download size:9.9MB

Instant FileName:gromacs-4.6.1-tar.gz

Renewed:March 10, 2013

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Cost: free

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History updates (Complete changelogs since the listing on this site)

4.6.1 [03-10-13]

made cool quotes database plain text
fixed invalid read in constructing N-centered vsites
changed treatment of fftpack source files to only build when they're used

Other versions : 4.6 4.5.5

v4.6 [01-27-13]

Fixed trjconv not writing velocities with cpt input
Fixed incorrect TPI results with dynamic box
Fixed DD charge group displacement error check
Fixed segv/hang with EM and foreign lambda values
Fixed mdrun -cpi, SD and pcoupl initialization
Fixed dispersion correction with parallel EM
Fixed initial COM motion removal with multiple groups
Fixed segfault in graph code with coordinate subsets
Allow -append to overrule unsupported file locking
Added correction for PME virial with non-linear virtual sites
Fixed increasing memory usage with SHAKE and DD
Fixed g_anaeig incorrect multiple extremes, fixes http://redmine.gromacs.org/issues/870
Added check for mass-weighting with g_anaeig -entropy, fixes http://redmine.gromacs.org/issues/785
Fixed array index out of bounds in EM force trr storage
Fixed bug with COM motion removal on part of the system
Fixed pull constraint periodicity consistency check, fixes http://redmine.gromacs.org/issues/844
Fixed pull constraining doing nothing, fixes http://redmine.gromacs.org/issues/825
Fixed segv in parallel replica exchange
Fixed http://redmine.gromacs.org/issues/1035 - NaN in g_cluster output.
Fixed bug in g_hbond that makes it produce fatal error.
Fixed http://redmine.gromacs.org/issues/593 about memory hole in trjcat.
Set return value to FALSE (0) in estimate_dt in libxdrf.c
Adapted NMR related data to new pdb format.
Made tutorial slightly less confusing.
Optional computation of fluct. props in g_energy. Fixes http://redmine.gromacs.org/issues/954
Fixed http://redmine.gromacs.org/issues/961 - Shake reports wrong error
Fixed http://redmine.gromacs.org/issues/882 - looping bug in trxio.c
Introduced fatal error in grompp for incorrect use of settle and charge groups.
Commented out part of this new program g_dos that was not yet validated, in order to protent users from incorrect results.
Fixed http://redmine.gromacs.org/issues/681 - Added warning line to terminal output about interpretation of results.
g_select now works in double precision (http://redmine.gromacs.org/issues/850).
g_select now works better with PDB files (http://redmine.gromacs.org/issues/916, http://redmine.gromacs.org/issues/1007)
Fixes to bugs with complex selections in g_select that could cause crashes or incorrect selections (http://redmine.gromacs.org/issues/968, http://redmine.gromacs.org/issues/1004, http://redmine.gromacs.org/issues/1006).
Fixed memory error in g_anaeig -proj that could cause crashes or incorrect results.
Fixed timing measurements with md-vv. (b03f3ad)
Fix large file support (for Windows)
Fix rerun in parallel with md-vv
Serveral minor cmake fixes
Fix domain decomposition setup for >46k cores
Fix g_dist for non-matching tpr/xtc
Correct results for FFT length which are multiples of 12 with internal FFT (fftpack - GMX_FFT_LIBRARY=fftpack). Affects mdrun if one of the fourier_n? option is multiple of 12. Also can affect tools using FFT if input size is multiple of 12 (g_densorder, g_hydorder, g_dos, g_hbond, g_dielectic).
Made g_tune_pme work correctly when init_step > 0 in the .mdp file
Essential dynamics: fixed a rare bug that could prevent a multi-molecule ED group from staying in the correct periodic representation when running on a single node. Also fixed calculation of the eigenvector projection if a target and/or origin structure was given in make_edi for cases where the fit structure is not the average structure.
Fixed crash in g_dist
Fixed .g96 trajectory reading
Removed warnings during compile on gcc 4.6+
Fixed potential crash in g_bar
Support for atomic operations assembly on llvm
Enhanced support for thread affinity on Linux
Fixed various things in trjconv, including -sub with .trr files http://redmine.gromacs.org/issues/1118
Added check for valid wall_atomtype in .mdp files http://redmine.gromacs.org/issues/700
Added fatal error to prevent use of the erroneous md-vv integrator and v-rescale thermostat combination http://redmine.gromacs.org/issues/1000
Added fatal error to prevent use of L-BFGS minimizer with constraints http://redmine.gromacs.org/issues/1053
Fixed REMD with distance restraints http://redmine.gromacs.org/issues/613
Corrected REMD citation
Added known bug that gmxdump -s -sys does not deal correctly with position restraints http://redmine.gromacs.org/issues/635
Improved pdb2gmx output when generating hydrogen atoms and termini
Partial fix of endian-ness testing http://redmine.gromacs.org/issues/944
Minor fixes for BlueGene systems
Added BlueGene/P CMake toolchain file
Various improvements to warnings, error messages, documentation, etc.
Documented the function of g_cluster -cl -noav
Added warning against equilibrating with Parinello-Rahman pressure coupling
Fixes to permit ThreadMPI to function on Cygwin http://redmine.gromacs.org/issues/833
Fix to trigger correct hardware acceleration on Cygwin
Fixed g_lie counting last frame twice
Fixes for pdb2gmx -cmap with multiple chains or to non-peptide residues http://redmine.gromacs.org/issues/800, http://redmine.gromacs.org/issues/885
Fixed g_sham when using more than 3 dimensions
Fixed g_mindist -o http://redmine.gromacs.org/issues/872
Fixed and documented g_angle and g_chi assumptions about trajectory period when counting transitions
Fixed g_angle -ot without -type dihedral
Fixed g_angle -f -or to copy times from -f to -or
Fix for GB+double+SSE2+accelerated kernels
Added TIP4P back into CHARMM27
Made g_helix sensitive to CHARMM27 atom naming http://redmine.gromacs.org/issues/896
Fix for CHARMM27 zinc ion to have charge +2
Fix such that CMake only warns about the OpenMPI version when it is old enough to be of concern
Fix to build of sse kernels in cmake if acceleration was set manually

v4.5.5 [12-29-11]

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The doDownload.com constantly monitors the update of all programs, including information from the Gromacs 4.6.2 changelog file, however sometimes it can happen that data are not complete or are outdated.We assume that author continue's to develop 4.7.0 version with further advanced features, and soon you will be informed. Equally important 5.0.0 upgrades of the program we will continue to monitor. Full Gromacs description has been compared with the overall software database and our algorithm has found the following applications (are showed below).

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