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GROMACS 4.0

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So,

First the bad news: from now on we're probably not going to care too much about bugs in gromacs-3.3.

The good news is that Gromacs 4.0 is finally & officially _released_.

You can download the source code package at

ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.tar.gz

We will put documentation and binary packages online early next week, but before doing that we figured we might give the early adopters a chance to compile it from source, just in case there's something that needs fixing...

Have fun with it!

Cheers,

Erik

Changes for GROMACS 4.0

The major change for GROMACS 4.0 is the domain decomposition which provides two orders of magnitude better scaling. The details on the new algorithms can be found in the GROMACS 4 paper J. Chem. Theory Comput. 4, 435 (2008).

New features

* Domain decomposition provides two orders of magnitude better scaling.
Parallel simulations can be started with grompp and mpirun -np mdrun without further options. For high parallelizations some options might improve the performance, see the pdf manual and mdrun -h.
* The steepest descents and conjugate gradients minimizers now also work in parallel.
* Full checkpointing support for exact continuation of simulations. mdrun reads checkpoint files. tpbconv is no longer required.
* mdrun option -maxh for terminating the simulation after a certain number of hours, very useful for queuing systems.
* Complete rewrite of the pull code: several new features, the options are integrated into the mdp file and the code now also works in parallel.
* Support for tabulated bonded interactions, especially useful for coarse-grained simulations.
* Support for heuristic neighborlist updates: the neighborlist uses a buffer region and it is updated when it becomes invalid, this provides exact integration.
* Several new PME and reaction-field electrostatics options for use with heuristic neighborlist updates.
* Improved energy conservation for all constraint algorithms.
* New velocity rescaling thermostat of Bussi et al. provides a true canonical ensemble together with the advantages of the Berendsen thermostat.
* Automated solute free energy (de)coupling with mdp options (no more messing with topologies).
* With replica exchange each replica can now be run in parallel.
* Optimized force loops for the IBM Blue Gene increase the performance by a factor of 2.
* New tpr file format is 5 times smaller (old tpr files can still be read). This format makes grompp orders of magnitude faster for systems of millions of atoms.
* Reduction of the memory usage of mdrun by a factor of 5, this is especially important for the Blue Gene.
* Several new analysis tools.

Resolved issues

* Much stricter checking of mdp options in grompp, grompp now by default terminates when there is one warning. There are now also notes which suggest better mdp settings.
* The box shape drift, which could only be observed over hundreds of nanoseconds, has been removed.
* Parrinello-Rahman pressure coupling would not scale the coordinates, this has been fixed, now the energy is conserved.
* The coupling time for the Parrinello-Rahman barostat was scaled by the pressure factor 16.6, now this has been fixed make sure that the coupling period tau_p is large enough.
* A stability problem with virtual sites for all-atom force fields has been resolved. Now also all-atom force fields are stable with a time step of 5 fs, this requires running pdb2gmx to generate a new topology file.
* The checkpoint file stores all the state variables, including the random state for SD and BD, so it is no longer necessary to change the seed in the mdp file for run continuation without repeating random numbers.

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