PLUMED-NEST

Project ID: plumID:19.017
Source: plumed_metad/metad_28ang.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

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
The POSITION action with label sph_coord calculates the following quantities:
 Quantity   
 Description  
sph_coord.x
the x-component of the atom position
sph_coord.y
the y-component of the atom position
sph_coord.z
the z-component of the atom positionbnz_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

The POSITION action with label bnz_coord calculates the following quantities:
 Quantity   
 Description  
bnz_coord.x
the x-component of the atom position
bnz_coord.y
the y-component of the atom position
bnz_coord.z
the z-component of the atom positionabs_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
The MATHEVAL action with label abs_x calculates a scalar quantityabs_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
The MATHEVAL action with label abs_y calculates a scalar quantityabs_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

The MATHEVAL action with label abs_z calculates a scalar quantityrho: 
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
The MATHEVAL action with label rho calculates a scalar quantitytheta: 
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
The MATHEVAL action with label theta calculates a scalar quantityphi: 
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
The MATHEVAL action with label phi calculates a scalar quantityrestr: 
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
=2.8 
KAPPA
the force constant for the wall
=10000

# Coordination number
The UPPER_WALLS action with label restr calculates the following quantities:
 Quantity   
 Description  
restr.bias
the instantaneous value of the bias potential
restr.force2
the instantaneous value of the squared force due to this bias potentialc: 
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
The COORDINATION action with label c calculates a scalar quantity
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
=3.0,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


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
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