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)