Syntax in PLUMED 2 has been completely redesigned. The main difference is that whereas in PLUMED 1 lines could be inserted in any order, in PLUMED 2 the order of the lines matters. This is due to a major change in the internal architecture of PLUMED. In version 2, commands (or "actions") are executed in the order they are found in the input file. Because of this, you must e.g. first compute a collective variable and then print it later. More information can be found in the Section about Syntax.

Another very important change is in the way groups are used, discussed below. Finally, many features appear under a different name in the new version.

Groups

In Plumed 1 groups (lists) were used for two tasks:

To provide centers of masses to collective variables such as distances, angles, etc. This is now done by defining virtual atoms using either CENTER or COM
To provide lists of atoms to collective variables such as coordination, gyration radius, etc. This is now done directly in the line that defines the collective variable.

If you would still like to use groups you can use the GROUP commands. Whenever the label for a GROUP action appears in the input it is replaced by the list of atoms that were specified in the GROUP.

Directives

What follows is a list of all the documented directives of Plumed 1 together with their plumed 2 equivalents. Be aware that the input syntaxes for these directives are not totally equivalent. You should read the documentation for the Plumed 2 Action.

HILLS	METAD
WELLTEMPERED	METAD with BIASFACTOR
GRID	METAD with GRID_MIN, GRID_MAX, and GRID_BIN
WRITE_GRID	METAD with GRID_WFILE, GRID_WSTRIDE
READ_GRID	currently missing
MULTIPLE_WALKERS	METAD with options WALKERS_ID, WALKERS_N, WALKERS_DIR, and WALKERS_RSTRIDE
NOHILLS	not needed (collective variables are not biased by default)
INTERVAL	METAD with INTERVAL
INVERT	currently missing
PTMETAD	not needed (replica exchange detected from MD engine)
BIASXMD	not needed (replica exchange detected from MD engine); one should anyway use RANDOM_EXCHANGES to get the normal behavior
UMBRELLA	RESTRAINT
STEER	MOVINGRESTRAINT
STEERPLAN	MOVINGRESTRAINT
ABMD	ABMD
UWALL	UPPER_WALLS
LWALL	LOWER_WALLS
EXTERNAL	EXTERNAL
COMMITMENT	currently missing
PROJ_GRAD	DUMPPROJECTIONS
DAFED	currently missing
DISTANCE	DISTANCE
POSITION	currently missing
MINDIST	DISTANCES with keyword MIN (See also Calculating a minimum distance)
ANGLE	ANGLE
TORSION	TORSION
COORD	COORDINATION
HBOND	currently missing , can be emulated with COORDINATION
WATERBRIDGE	BRIDGE
RGYR	GYRATION
DIPOLE	DIPOLE
DIHCOR	currently missing , can be emulated with multiple TORSION combined with MATHEVAL
ALPHABETA	ALPHABETA
ALPHARMSD	ALPHARMSD
ANTIBETARMSD	ANTIBETARMSD
PARABETARMSD	PARABETARMSD
ELSTPOT	currently missing
PUCKERING	currently missing
S_PATH	PATHMSD, s component
Z_PATH	PATHMSD, z component
TARGETED	RMSD
ENERGY	ENERGY
HELIX	currently missing
PCA	currently missing
SPRINT	currently missing
RDF	DISTANCES, used in combination with HISTOGRAM / BETWEEN keyword
ADF	ANGLES, used in combination with HISTOGRAM / BETWEEN keyword
POLY	COMBINE
FUNCTION	MATHEVAL
ALIGN_ATOMS	WHOLEMOLECULES