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Unreleased.txt
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Unreleased.txt
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/**
@page CHANGES-UNRELEASED Unreleased changes
Include all fixes in branch 2.1 indicated in \ref CHANGES-2-1 .
Changes from version 2.1 which are relevant for users:
- Changes leading to incompatible behavior:
- Labels of quantities calculates by \ref SPRINT have changed from <i>label</i>.coord_<i>num</i> to <i>label</i>.coord-<i>num</i>
- \ref METAD with WALKERS_MPI now writes a single hills file, without suffixes
- removed the ./configure.sh script of v2.0.x, now plumed can only be configured using autotools (./configure)
- \ref COM, \ref CENTER, and \ref GYRATION now automatically make molecules whole. In case you do not want them to do it, use NOPBC flag,
which recovers plumed 2.1 behavior
- Added experimental OpenMP support, see \ref Openmp
- Added multiple time step integration for bias potentials, see \ref MTS
- Link cells are now used in all multicolvars that involve \ref switchingfunction. The link cell cutoff is
set equal to 2.*\f$d_{\textrm{max}}\f$. Where \f$d_{\textrm{max}}\f$ is the (user-specified) point at which
the switching function goes to zero. Users should always set this parameter when using a switching function
in order to achieve optimal performance.
- New actions
- \ref DUMPMASSCHARGE to dump a file with mass and charges during MD.
- \ref EFFECTIVE_ENERGY_DRIFT to check that plumed forces are not screwing the MD integrator.
- \ref EXTENDED_LAGRANGIAN : in combination with \ref METAD it implements metadynamics with Extended Lagrangian; standalone it implements TAMD/dAFED.
- \ref DFSCLUSTERING calculate the size of clusters
- \ref DUMPMULTICOLVAR print out a multicolvar
- \ref MFILTER_LESS filter multicolvar by the value of the colvar
- \ref MFILTER_MORE
- \ref MFILTER_BETWEEN
- \ref GRADIENT can be used to calculate the gradient of a quantity. Used to drive nucleation
- \ref CAVITY
- \ref PUCKERING implemebted for 5-membered rings (thanks to Alejandro Gil-Ley).
- \ref WRAPAROUND to fix periodic boundary conditions.
- New features for existing actions:
- Keywords UPDATE_FROM and UPDATE_UNTIL to limit update step in a defined time window.
- Keyword UNNORMALIZED for \ref HISTOGRAM.
- Keywords for \ref GROUP (REMOVE, SORT, UNIQUE) to allow more flexible editing of groups.
- \ref DUMPATOMS now supports dumping xtc and trr files (requires xdrfile library).
- \ref driver can now read xtc and trr files also with xdrfile library.
- \ref driver accepts a --mc flag to read charges and masses from a file produced during
molecular dynamics with \ref DUMPMASSCHARGE
- Possibility to enable or disable \ref RESTART on a per action basis.
- \ref MOLINFO now supports many more special names for rna and dna (thanks to Alejandro Gil-Ley).
- VMEAN and VSUM allow one to calculate the sum of a set of vectors calculated by VectorMultiColvar. Note these
can also be used in tandem with \ref AROUND or \ref MFILTER_MORE to calculate the average vector within a particular
part of the cell or the average vector amonst those that have a magnitude greater than some tolerance
*/