Project ID: plumID:21.043
Source: PLUMED-NEST/plumed-1.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.8
tested onmaster
#RESTART

FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=step5_charmm2gmx-modified.pdb a0:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=0,0,0 az:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=0,0,1 phi:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=70,143,a0,az theta:
TORSION
Calculate a torsional angle. More details
ATOMS
the four atoms involved in the torsional angle
=2549,2420,a0,az
##ZANGLES ATOMS=70,143 LABEL=phi ##ZANGLES ATOMS=2549,2420 LABEL=theta # Activate metadynamics in phi and psi # depositing a Gaussian every 500 time steps, # with height equal to 1.0 kJoule/mol, # and width 0.35 rad for both CVs.
METAD
Used to performed metadynamics on one or more collective variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=phi,theta
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=1.0
SIGMA
the widths of the Gaussian hills
=0.35,0.35
FILE
a file in which the list of added hills is stored
=HILLS
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.0
GRID_MIN
the lower bounds for the grid
=-pi,-pi
GRID_MAX
the upper bounds for the grid
=pi,pi
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1,0.1 ... METAD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
ARG
the input for this action is the scalar output from one or more other actions
=phi,theta,metad.bias
FILE
the name of the file on which to output these quantities
=COLVAR