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
In python interface, fixed usage of python arrays to allow compatibility with PyPy.