Version 2.7

Version 2.7.0 (Dec 23, 2020)

Changes from version 2.6 which are relevant for users:

  • Changes leading to differences with previous versions
    • The definition of the omega angle has been modified to adhere to the IUPAC standard (i.e. with the previous amino acid)
  • New contributed modules:
    • A new Funnel module by Stefano Raniolo and Vittorio Limongelli
    • A new Infinite Switch Simulated Tempering in Force module by Glen Hocky
    • A new OPES module by Michele Invernizzi
  • New actions:
  • Other improvements:
    • MOLINFO action can now be used multiple times. Every action doing a search will use the latest appearance. See #134.
    • Neighbor lists are now OpenMP and MPI parallel so improving the scalability of all actions employing them
    • It is now possible to pass pdb files with all weights set to zero. Instead of reporting an error, PLUMED will now assume they are all equal to 1/n, where n is the number of atoms (see #608).
    • All the examples in the manual are now displayed with contextual help and regularly tested for correctness.
    • A tool to build PLUMED input directly within a python script has been added (see #611 and documentation for class plumed.InputBuilder()).
    • Python function plumed.read_as_pandas() now also accepts an argument index_col.
    • Lepton arithmetics can be used also when reading integers (e.g., METAD PACE=2*5, see #614).
  • GROMACS:
    • When using -hrex flag, the neighbor lists are update automatically at every exchange step. This relaxes the requirements on the choice of -replex stride (see #579, thanks to Chang Junhan).
  • Changes in the DRR module
    • Support multi-time stepping. Now the STRIDE keyword should work with DRR correctly.
    • Support reflecting boundary conditions, which should be a better solution to the boundary effect of eABF in non-periodic cases. You can use REFLECTINGWALL to enable it.
    • Stop the simulation when the temperature is not passed from the MD engine to PLUMED. In this case, users should set the temperature by the TEMP keyword.
  • Changes in the ISDB module
    • There is a new option for OPTSIGMAMEAN, SEM_MAX that allows to automatically determine an optimal value for SIGMA_MAX
  • Changes in the VES module
    • Small changes to TD_MULTICANONICAL and TD_MULTITHERMAL_MULTIBARIC. Bug fix concerning the calculation of the logarithm of the target distribution. Added the keyword EPSILON to avoid dealing with regions of zero target probability.

For developers:

  • small fix in Plumed.h too avoid unique global symbols (see #549)
  • Added cmd("readInputLines") to allow reading input from a buffer with comments and continuation lines (see #571).
  • fixed error when the install prefix contained unicode characters

Version 2.7.1 (Apr 16, 2021)

  • Includes all fixes up to 2.6.3
  • In python interface, fixed usage of python arrays to allow compatibility with PyPy.
  • New/updated patches:
    • updated patch for gromacs-2020.5
    • new patch for gromacs-2021
      • this should work with multiple-time stepping (plumed forces are integrated with the smallest time step, plumed can internally implement a multiple-time step if needed).
      • Modular simulator is still not supported
      • hrex, lambda cv and replica-exchange are not yet tested

Version 2.7.2 (Jul 27, 2021)

  • Fixed a bug in the -hrex implementation for GROMACS 2020 and 2021 (see #691, thanks to Chang Junhan).
  • Changes in the OPES module
    • the CALC_WORK option now outputs the accumulated work, as in METAD, instead of the work done in the last bias update

Version 2.7.3

  • GROMACS patches now take a note of the used PLUMED version in the GROMACS log (see #737)