@@ -47,8 +47,8 @@ Changes from version 2.4 which are relevant for users:
-\ref pdbrenumber (see \issue{371}).
- Changes in the ISDB module
-\ref CS2BACKBONE is now mpi parallelised in particular with DOSCORE and CAMSHIFT
-\ref SAXS has an additional implementation based on bessel functions that can be faster for large systems (new keyword BESSEL)
-\ref CS2BACKBONE is now mpi parallelized in particular with DOSCORE and CAMSHIFT
-\ref SAXS has an additional implementation based on Bessel functions that can be faster for large systems (new keyword BESSEL)
-\ref SAXS keyword SCEXP has been renamed into SCALEINT
-\ref METAINFERENCE and all related methods has a new keyword REGRES_ZERO to scale data using a linear scale fit
-\ref CALIBER new bias to perform Maximum Caliber replica-averaged restrained simulations
...
...
@@ -68,12 +68,12 @@ Changes from version 2.4 which are relevant for users:
- Other changes:
-\ref METAD there is a new FLYING_GAUSSIAN keyword to activate the flying gaussian methods by Spiwok (contributed by Spiwok and Hozzova)
-\ref EXTERNAL can now SCALE the input grid. This allows for more flexibility without modifying the grid file.
-\ref ALPHABETA can now combine dihedrals with different coefficients
-\ref ALPHABETA can now combine dihedral angles with different coefficients
-\ref INCLUDE can now be used also before setup actions.
-\ref CENTER can now be computed using trigonometric functions (PHASES) to simplify its calculation with PBCs.
-\ref CENTER can now be computed using trigonometric functions (PHASES) to simplify its calculation with periodic boundary conditions.
- Libmatheval is not used anymore. \ref MATHEVAL (and \ref CUSTOM) are still available
but employ an internal implementation of the lepton library.
Functions available in libmatheval and absent in the original lepton library have been added so as to have backward compatbility.
Functions available in libmatheval and absent in the original lepton library have been added so as to have backward compatibility.
`atan2(y,x)` function has also been added.
Notice that MATHEVAL (and CUSTOM) \ref switchingfunction "switching functions"
using the lepton library have been further optimized with respect to PLUMED 2.4.
...
...
@@ -82,7 +82,7 @@ Changes from version 2.4 which are relevant for users:
-\ref MOLINFO now allows selecting atoms from chains with a numeric ID (see \issue{320}).
- Removed the patch for GMX 5.1.4
-\ref RMSD calculation has been optimized. This should positively affect the performances of CVs where
many RMSDs are computed on small groups of atoms, such as secondary structure variables.
many RMSD values are computed on small groups of atoms, such as secondary structure variables.
- In \ref METAD, when using a bias factor equal to one (no bias) the `rct` component is set to zero rather than to one.
- New shortcuts are available for selecting atoms: `@allatoms` and `@mdatoms` (see \ref atomSpecs).
- When using \ref MOLINFO, also the following shortcuts are available for selecting atoms: `@nucleic`, `@protein`, `@water`, `@ions`, `@hydrogens`, `@nonhydrogens`.
...
...
@@ -110,8 +110,8 @@ Changes from version 2.4 which are relevant for developers:
- Exception class has been rewritten to allow more extensive messages. Now also function name is shown.
- On linux, library is linked with `-Bsymbolic`.
- A small number of header files is installed
- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearence is the effective one.
- Internal blas and lapack libraries updated to gromacs 2018.
- When launching `plumed`, flags `--no-mpi` and `--mpi` can appear multiple times. The last appearance is the effective one.
- Internal BLAS and LAPACK libraries updated to gromacs 2018.
- Choosing `./configure --prefix=$PWD` does not lead anymore to deletion of all header files.
- Runtime loader in `Plumed.c` now works also when linked without `-rdynamic` (that is,
its names are not exported). Notice that all the combinations are expected to
