New and improved features#
Changed to require a C++11 compiler#
GROMACS now requires both a C++11 and C99 compiler. For details, see the install guide.
Changed to support only CUDA 5.0 and more recent versions#
Allowed rcoulomb > rvdw with PME#
GROMACS has had kernels that support Coulomb PME + cut-off LJ with rcoulomb > rvdw for a while, but these were only available via PME load balancing. Now we allow this setup to be chosen also through mdp options.
Added optional support for portable hardware locality (hwloc)#
Added CMake support to detect and build GROMACS with hwloc, which will improve GROMACS ability to recognize and take advantage of all the available hardware. If hwloc is unavailable, GROMACS will fall back on other detection routines.
Made normal-mode calculations work with shells and vsites#
Implemented shells and vsites in normal-mode analysis in mdrun and in analysis of eigenvalues and frequencies. The normal-mode analysis is done on real atoms only and the shells are minimized at each step of the analysis.
Changed pull group count for coords stored in tpr file#
Added a parameter ngroup to the pull coord parameters. This is now also stored in the tpr file. This makes the pull geometry forward compatible, which is useful since it avoid bumping the .tpr version with every new geometry, and we expect that users want to experiment with new geometries.
Added pull coordinate geometry angle-axis#
The new geometry is described in the docs. Some checks in readpull.cpp where reorganized since adding new geometries made some old logic a bit convoluted.
Added pull coordinate geometry dihedral (angle)#
How to use the new geometry is explained in the docs.
Added pull coordinate geometry angle#
A new subsection was added to the docs explaining the new geometry.
pull-print-com1,2 mdp option with
Changes were made to the pull output order and naming.
Added pull potential flat-bottom-high#
Added the new pull coordinate type flat-bottom-high, which is a flat potential above the reference value and harmonic below.
gmx grompp check for pull group#
Added a check for valid pull groups in a pull coordinate. Using a pull group index that was out of range would cause invalid memory access.
Added new swapping functionality to computational electrophysiology module#
Support was added for ion/water position swapping for multiple ion types and polyatomic ions, including use of a user-defined number of ionic species, and (small) polyatomic ions.
Also added two extra .mdp file parameters ‘bulk-offset’ that allow the user to specify an offset of the swap layers from the compartment midplanes. This is useful for setups where e.g. a transmembrane protein extends far into at least one of the compartments. Without an offset, ions would be swapped in the vicinity of the protein, which is not wanted. Adding an extended water layer comes at the cost of performance, which is not the case for the offset solution.
Documentation and testing was improved.
Fixed logic for DD missing-interactions check#
The code that was intended to double check that the domain decomposition algorithm has not missed any interactions was inactive in several cases, and has been fixed.
Permitted forces and velocities to be written to compressed TNG#
If there is no uncompressed coordinate output, write forces and velocities to the TNG file with compressed coordinate output. If there is uncompressed coordinate output to a TNG file, forces and velocities will be written to it.
Use a greatest common divisor to set the frequency of some TNG data output to ensure lambdas and box shape are written at least as often as anything else.
Added mdrun check for finite energies#
Added a check that the total potential energy is finite. This check is nearly free and can catch issues with incorrectly set up systems before users get a confusing constraint or PME error. Note that this check is only performed at steps where energies are calculated, so it will often not catch an exploding system.
gmx grompp check for unbound atoms#
gmx grompp now prints a note for atoms that are not connected by a
potential or constraint to any other atom in the same moleculetype,
since this often means the user made a mistake.
Improved multi-simulation signalling#
Multi-simulations (including REMD) may have need to send messages
between the simulations. For example, REMD needs to write a
fully-consistent set of checkpoint files so that the restart works
correctly, but normal multi-simulations are fine with decoupled
progress and will simulate more efficiently if they can do
gmx_mpi mdrun -maxh -multi needs to synchronize
only for REMD. The implementation has been upgraded so that such
coupling happens only when an algorithm chosen by the user requires
Issue 860, Issue 692, Issue 1857, Issue 1942
Changed multi-simulation nsteps behaviour “”””””””””””””””””””””””””””””””””””””””””””””””””””””””””””””””””-
It is unclear what the expected behaviour of a multi-simulation should be if the user supplies any of the possible non-uniform distributions of init_step and nsteps, sourced from any of .mdp, .cpt or command line. Previously mdrun adjusted the total number of stesps to run so that each run did the same number of steps, but now it reports on the non-uniformity and proceed, assuming the user knows what they are doing.
Added working directory to things reported in .log file#
When running GROMACS via a batch script, it is useful to know which working directory is being used for relative paths (file names) in the command line. This is now written alongside other header information.
Prevented fragile use cases involving checkpoint restarts and/or appending#
All output files named in the checkpoint file (ie. that were
used in the previous run) must be present before a checkpoint
restart will be permitted. Thus,
workflows where people used things like
gmx mdrun -s production -cpi equilibration
are no longer available to do a “continuous” restart. Instead, use
gmx grompp -t equilibration -o production.
Removed warning after OpenMP core-count check#
In many cases
gmx_mpi mdrun issued a warning that compared the total
core count with something different returned from OpenMP. This problem
is caused by inappropriate management of thread affinity masks, but
the wording of the message did not help the user realise this, so has
gmx_mpi mdrun -pin on may help improve performance in
Preparation for hardware detection might try to force offline cores to work#
Hardware detection might be foiled by kernels that take cores offline when work is unavailable. We are not aware of any such platforms on which GROMACS is likely to be used, but we will probably start to see them soon. On such platforms, if the number of cores physically present differs from the count that are online, we try to force them online before deciding how GROMACS will use the online cores. For now, no x86 or PowerPC platforms need such code, so it will never run on those platforms. The good news is that we no longer have to risk making a confusing warning about such possibilities.
Added new suggestion for users to try e.g. hyper-threading, if its disabled#
GROMACS tends to perform best with several hardware threads available per core (e.g. hyper-threading turned on, on x86), and now the log file will note explicitly when such opportunities exist.