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 onv2.9
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