Version 2.4

Version 2.4 (Dec 15, 2017)

Version 2.4 contains several improvements with respect to 2.3. Users currently working with 2.3 should have a look at the section "Changes leading to incompatible behavior" below and might need tiny adjustments in their input files. Notice that version 2.4 includes already all the fixes in branch 2.3 up to 2.3.3 indicated in Version 2.3 .

Changes from version 2.3 which are relevant for users:

• Changes leading to incompatible behavior:
  • A c++11 compliant compiler is required (see #212). This should mean:
    • gcc 4.8
    • clang 3.3
    • intel 15 Since the number of c++11 features that we use is limited, older compilers might work as well.
  • The meaning of BIASFACTOR=1 in METAD has been modified and can now be used to indicate unbiased simulations. Non-well-tempered metadynamics is BIASFACTOR=-1, which is the new default value. Notice that this has an implication on the bias factor written in the HILLS file when doing non-well-tempered metadynamics.
  • Due to a change in COMMITTOR, the format of its output file has been slightly changed.
  • HISTOGRAM : When using weights default is now to output histogram divided by number of frames from which data was taken. In addition the UNORMALIZED flag has been replaced with the keyword NORMALIZATION, which can be set equal to true, false or ndata.
  • All switching functions are now stretched by default, also when using the "simple syntax" (e.g. COORDINATION NN=6). Switching functions were already stretched by default when using the advanced syntax (e.g. COORDINATION SWITCH={}) since version 2.2. Notice that this will introduce small numerical differences in the computed switching functions.
• New modules:
  • A new PLUMED-ISDB module have been included, this module includes a number of CVs to calculate experimental data with the internal ability to also calculate a METAINFERENCE score.
    • New actions include:
      • EMMI
      • SAXS
      • RESCALE, SELECT, SELECTOR
    • Updated actions include:
      • CS2BACKBONE
      • FRET
      • JCOUPLING
      • METAINFERENCE
      • NOE
      • PRE
      • RDC, PCS
      • PBMETAD
  • A new EDS module have been included, contributed by Glen Hocky and Andrew White. This module implements the following methods:
    • EDS
  • A new DRR module have been included, contributed by Haochuan Chen and Haohao Fu. This module implements the following methods:
    • DRR
    • drr_tool
  • A new VES module have been included, contributed by Omar Valsson. This module implements the following methods:
    • BF_CHEBYSHEV
    • BF_COMBINED
    • BF_COSINE
    • BF_CUSTOM
    • BF_FOURIER
    • BF_LEGENDRE
    • BF_POWERS
    • BF_SINE
    • OPT_AVERAGED_SGD
    • OPT_DUMMY
    • TD_CHI
    • TD_CHISQUARED
    • TD_CUSTOM
    • TD_EXPONENTIAL
    • TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
    • TD_GAUSSIAN
    • TD_GENERALIZED_EXTREME_VALUE
    • TD_GENERALIZED_NORMAL
    • TD_GRID
    • TD_LINEAR_COMBINATION
    • TD_PRODUCT_COMBINATION
    • TD_PRODUCT_DISTRIBUTION
    • TD_UNIFORM
    • TD_VONMISES
    • TD_WELLTEMPERED
    • VES_LINEAR_EXPANSION
    • VES_OUTPUT_BASISFUNCTIONS
    • VES_OUTPUT_FES
    • VES_OUTPUT_TARGET_DISTRIBUTION
    • ves_md_linearexpansion
• New collective variables:
  • DIMER (thanks to Marco Nava).
  • EEFSOLV : EEF1 implicit solvent solvation energy
  • ADAPTIVE_PATH : Adaptive path variables using the method from [82]
• New actions:
  • INENVELOPE
  • TOPOLOGY_MATRIX
  • BOND_DIRECTIONS
  • DUMPGRAPH
  • GRID_TO_XYZ
  • INTEGRATE_GRID
  • LWALLS
  • MAXENT
  • MCOLV_COMBINE
  • MCOLV_PRODUCT
  • POLYMER_ANGLES
  • XANGLES , YANGLES , ZANGLES
  • XYTORSIONS , XZTORSIONS , YXTORSIONS , YZTORSIONS , ZXTORSIONS , and ZYTORSIONS
• New command line tools:
  • pesmd : Tool for performing Langevin dynamics on an energy landscape that is specified using a PLUMED input file
  • pathtools
• Other changes:
  • Sharing coordinates and applying force is now faster (in some cases these can result in much better scaling of the performances in parallel).
  • COMMITTOR : new flag to use committor to keep track of the visited basins without stopping the simulation
  • PBMETAD : multiple walkers using files (thanks to Marco De La Pierre).
  • PBMETAD : adaptive Gaussian kernels
  • PBMETAD : default names for GRID and FILE (useful with many collective variables)
  • METAD : BIASFACTOR=1 is allowed and performs unbiased sampling. HILLS file can be used to recover free energy also in this case.
  • METAD : a RECT option is available that allows setting an array of bias factors, one for each replica.
  • METAD : added options to perform Transition Tempered Metadynamics (thanks to James Dama)
  • PATHMSD and PROPERTYMAP now support alignment to a close structure (thanks to Jana Pazurikova)
  • PDB files with more than 100k atoms can now be read using hybrid 36 format, see #226.
  • Added lepton support. Set env var export PLUMED_USE_LEPTON=yes to activate lepton as a matheval replacement in MATHEVAL, CUSTOM, and MATHEVAL switching function. Notice that in v2.5 matheval support will be dropped and all these keywords will use lepton. See #244.
  • When parsing constants, PLUMED uses lepton library. This allows to pass arguments such as HEIGHT=exp(0.5) (see Parsing constants).
  • CUSTOM function has been added as an alias to MATHEVAL .
  • Trajectories read in driver also support the usual replica convention, that is if trajectory with replica suffix is not found the driver will look for a trajectory without the replica suffix.
  • A new syntax (@replicas:) can be used to specify different arguments for different replicas (see Special replica syntax).
  • Internal molfile implementation has been updated to VMD 1.9.3.
  • Examples in the documentation now have syntax highlighting and links to the documentation of used actions.
  • COORDINATIONNUMBER : Added option to have pairwise distance moments of coordination number in the multicolvar module
  • GROMACS patch updated to gromacs-2016.4
  • Implemented HREX for gromacs-2016.4.
  • Added patch for Quantum ESPRESSO 6.2 (thanks to Ralf Meyer).
  • Fixed a bug in LOCAL_AVERAGE which appears when you use SPECIESA and SPECIESB keywords instead of just SPECIES
  • Added possibility to pass --kt from driver.

Changes from version 2.3 which are relevant for developers:

• A few fixes has been made to improve exception safety. Although we still cannot declare PLUMED totally exception safe (there are still many non-safe pointers around), this made it possible to add a regtest that actually tests erroneous cmd strings and erroneous inputs.
• Due to the required c++11 support, travis-ci test on Ubuntu Precise has been removed.
• gettimeofdate and gettime have been replaced with portable chrono classes introduced in c++11.
• C++ exceptions are enabled by default.
• A large number of loops have been changed to use the auto keyword in order to improve code readability.
• Stack trace is not written upon error anymore, unless environment variable PLUMED_STACK_TRACE is set at runtime.
• Fixed a potential bug using single precision system BLAS on a mac (notice that currently plumed only uses double precision, so it is harmless).
• Added --enable-rpath option for autoconf (off by default).
• Files related to changelog are now stored as .md files. This makes it possible to navigate them from github.
• configure.ac has been simplified and improved in order to more easily probe C++ libraries.
• added plumed_custom_skip function to regtests in order to skip specific tests based on specific conditions (e.g. OS).
• environment variable LDSO has been renamed to LDSHARED, which is standard in the python community.
• a libplumedWrapper.a library is installed as well, that is used in --runtime patching.
• pkgconfig files are installed.
• plumed config makefile_conf can be used to retrieve Makefile.conf file a posteriori.
• Store MPIEXEC variable at configure time and use it later for running regtests. Notice that in case MPIEXEC is not specified regtests will be run using the command stored in env var PLUMED_MPIRUN or, if this is also not defined, using mpirun.
• Added canonical Makefile targets check and installcheck. Notice that check runs checks with non-installed plumed whereas installcheck uses the installed one, including its correct program name if it was personalized (e.g. with suffixes). Notice that this modifies the previously available check target.

Version 2.4.1 (Mar 2, 2018)

For users:

• Fixed an important bug affecting RMSD calculations with compilers supporting OpenMP 4 (e.g.: intel compiler). Notice that this bug might potentially affect not only RMSD variable, but also PATHMSD variables using RMSD, FIT_TO_TEMPLATE, PCAVARS, and possibly other variables based on RMSD calculations and optimal alignments (see #343). Results might depend on the exact architecture and on how aggressive is the compiler. The bug is a consequence of some erroneous SIMD directives introduced in 2.4.0, so it does not affect PLUMED 2.3.x.
• Resolved a problem with CS2BACKBONE and glycine atom names.
• Module VES: Fixed a bug with basis functions that have a constant function different from 1 (e.g. scaled version of the Legendre basis functions, BF_LEGENDRE) that was causing a time-dependent shift in the bias potential.
• Module VES: In optimizers (OPT_AVERAGED_SGD and OPT_DUMMY) the output of quantities related to the instantaneous gradients are now off by default as these quantities are generally not useful for normal users, their output can instead by re-enabled by using the MONITOR_INSTANTANEOUS_GRADIENT keyword. Also added an keyword MONITOR_AVERAGE_GRADIENT that allows to monitor the averaged gradient and output quantities related to it.
• RMSD variable and other collective variables using reference PDB files now crash when zero weights are passed (see #247).
• Using COM with driver without passing masses now triggers an error instead of reporting NaNs (see #251).

For developers:

• plumed patch -p command can be used twice without triggering an error. This will allow e.g. building again on MacPorts in cases where the build was interrupted. Notice that this only works for patches without special after/before patch/revert functions.

Version 2.4.2 (Jul 2, 2018)

For users:

• All fixes done in version 2.3.6. Notice that #363 in version 2.4 also applies to pathtools.
• Additional residue names (without the prefix D) are now supported by MOLINFO for DNA. See #367.
• Solved an important bug appearing in NAMD interface. Notice that the bug was a regression introduced in 2.4.0. As consequence, versions <= 2.3 and versions >=2.4.2 are expected to work correctly. See #254.
• GROMACS patch for gromacs-2018.1.
• Using VIM syntax file now highlights __FILL__ strings.
• METAD and PBMETAD give a warning when one restarts a simulation and the old hills file is not found. See #366.

For developers:

• LDSHARED is now correctly taken into account when launching ./configure.
• Fixed installation with --disable-shared.
• Cppcheck upgraded to 1.84.

Version 2.4.3 (Oct 5, 2018)

For users:

• All fixes done in version 2.3.7.
• Module VES: Fixed a bug in TD_GRID for 2D grids where the grid spacing is not the same for both dimensions.
• GROMACS patch for gromacs-2018.3.

Version 2.4.4 (Dec 19, 2018)

For users:

• Fixed some performances regression issue with OpenMP
• Updated NAMD patches to version 2.12 and 2.13. Old patches have been removed.
• GROMACS patch for gromacs-2018.4.
• Fixed a thread safety issue using forces on HISTOGRAM
• Fixed error message suggesting wrong actions (see #421).

For developers:

• All fixed done in version 2.3.8
• Cppcheck updated to 1.85

Version 2.4.5 (Apr 1, 2019)

For users:

• Fixed an inconsistency in parsing of braces. It is now possible to pass individual options including spaces (e.g. with FILE={/path with space/file}). Notice that this invalidates syntax such as ATOMS={1}{2}{3}{4}. See more at #434.
• Fixed simplemd so as to call "runFinalJobs" at the end of the simulation.
• GROMACS patch for gromacs-2016.6.
• GROMACS patch for gromacs-2018.6.
• Added aliases for some actions/options containing dashes (-) in their name. This will improve backward compatibility when these actions/options will be removed (see #449).

Version 2.4.6 (Jul 19, 2019)

For users:

• Fixed a bug in COORDINATIONNUMBER where derivatives were wrong when using R_POWER > 2, thanks to @MoleOrbitalHybridAnalyst for spotting and fixing
• Fixed a bug in library search, possibly affecting linked blas/lapack on OSX (see #476).
• Fixed a bug in METAD with TARGET and GRID_SPARSE (see #467).

Version 2.4.7 (Jan 27, 2020)

For users:

• Fixed a bug with CONVERT_TO_FES and periodic variables, see #441 (backported from v2.5.3).
• More robust backup for output files when running over multiple processes
• Fixed a regression in the performances of GEOMETRY based flexible hills in METAD and PBMETAD
• Fixed #538.
• Fixed potential issue with VMD plugins from 1.9.4 (#545, thanks to Lixin Sun).
• Module VES: Fixed an off-by-one bug in the output of target distribution averages. The bug only affects the output and does not affect results. The bug also affected the output of coefficients when using a bias cutoff.
• Module VES: Made sure that all relevant output files are written out at the final step when shutting down the simulation. This solves issues reported by @PabloPiaggi with restarting when there is a mismatch been the output of files and the number of MD steps.

Version 2.4.8 (Jul 8, 2020)

Warning

This branch is not maintained. Users are invited to upgrade to a newer version

For users:

• Take into account UNITS when using MD codes that feeds one line at a time to PLUMED (e.g., OpenMM). See #582.
• Fix PDB parser for non justified atom numbers. See #592.
• Fix in INPLANEDISTANCES. See #595.

For developers:

• Tests and doc building moved from Travis-CI to GitHub Actions (see #634).