Project ID: plumID:19.017
Source: plumed_metad/metad_20ang.dat
Originally used with PLUMED version: 2.5
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
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
ENTITY0
the atoms that make up a molecule that you wish to align
=1-2593
ENTITY1
the atoms that make up a molecule that you wish to align
=2594-2605
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
=../input/heavy_atoms.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL
# Group definition prot_noh:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H sph:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=sphere bnz:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=BNZ_noH
WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
ATOMS
wrapped atoms
=bnz
AROUND
reference atoms
=sph
sph_center:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=sph bnz_center:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=bnz
sph_coord:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=sph_center
NOPBC
ignore the periodic boundary conditions when calculating distances
bnz_coord:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=bnz_center
NOPBC
ignore the periodic boundary conditions when calculating distances

abs_x:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=bnz_coord.x,sph_coord.x
FUNC
the function you wish to evaluate
=x-y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO abs_y:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=bnz_coord.y,sph_coord.y
FUNC
the function you wish to evaluate
=x-y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO abs_z:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=bnz_coord.z,sph_coord.z
FUNC
the function you wish to evaluate
=x-y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
rho:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=abs_x,abs_y,abs_z
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y+z*z
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO theta:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=abs_z,rho
FUNC
the function you wish to evaluate
=acos(x/y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=0.,pi phi:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input for this action is the scalar output from one or more other actions
=abs_x,abs_y
FUNC
the function you wish to evaluate
=atan2(y,x
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-pi,pi
# Restraining potential of the sphere restr:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=rho
AT
the positions of the wall
=2.0
KAPPA
the force constant for the wall
=10000
# Coordination number c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=bnz
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=prot_noh
R_0
The r_0 parameter of the switching function
=0.45
# Metadynamics
METAD
Used to performed metadynamics on one or more collective variables. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=rho,theta,phi
GRID_MIN
the lower bounds for the grid
=0,0.,-pi
GRID_MAX
the upper bounds for the grid
=2.2,pi,pi
SIGMA
the widths of the Gaussian hills
=0.1,pi/16.,pi/8
HEIGHT
the heights of the Gaussian hills
=1.2
PACE
the frequency for hill addition
=500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=rho
FILE
the name of the file on which to output these quantities
=distance.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=metad
FILE
the name of the file on which to output these quantities
=metad_data.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=restr
FILE
the name of the file on which to output these quantities
=sphere_restraint.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=abs_x,abs_y,abs_z
FILE
the name of the file on which to output these quantities
=xyz_coord.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=rho,theta,phi
FILE
the name of the file on which to output these quantities
=rtp_coord.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=c
FILE
the name of the file on which to output these quantities
=all_coordination_45.dat
STRIDE
the frequency with which the quantities of interest should be output
=500
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
STRIDE
the frequency with which all the open files should be flushed
=500