Project ID: plumID:21.018
Source: plumed_metad/metad_35ang_para.dat
Originally used with PLUMED version: 2.6
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
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
=1-3677
ENTITY1
the atoms that make up a molecule that you wish to align
=3678-3734
# 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/MacroD2_para_input/ref_index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H ref:
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/MacroD2_para_input/ref_index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Prot_ref_noH AR6:
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/MacroD2_para_input/ref_index.ndx
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=AR6_noH
ref_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
=ref AR6_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
=AR6
Fix:
FIXEDATOM
Add a virtual atom in a fixed position. More details
AT
coordinates of the virtual atom
=5.0,5.0,5.0 Dis:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=ref_center,Fix
ref_coord:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=ref_center
NOPBC
ignore the periodic boundary conditions when calculating distances
AR6_coord:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=AR6_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 to this function
=AR6_coord.x,ref_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 to this function
=AR6_coord.y,ref_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 to this function
=AR6_coord.z,ref_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
rel_x:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=abs_z,abs_y
FUNC
the function you wish to evaluate
=(x-y)/sqrt(2
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO rel_y:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=abs_x
FUNC
the function you wish to evaluate
=x
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO rel_z:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=abs_z,abs_y
FUNC
the function you wish to evaluate
=(x+y)/sqrt(2
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 to this function
=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 siga:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=rel_z,rho
FUNC
the function you wish to evaluate
=sqrt(-x+y
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 to this function
=rel_x,rel_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
rmsd:
RMSD
Calculate the RMSD with respect to a reference structure. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../input/MacroD2_para_input/ref_protein_noH_nosite.pdb
TYPE
the manner in which RMSD alignment is performed
=SIMPLE
# Restraining potential of the sphere restr_dis:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=Dis
AT
the positions of the wall
=1.00
KAPPA
the force constant for the wall
=20000
OFFSET
the offset for the start of the wall
=0 restr_rho:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=rho
AT
the positions of the wall
=3.50
KAPPA
the force constant for the wall
=20000
OFFSET
the offset for the start of the wall
=0 restr_siga:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=siga
AT
the positions of the wall
=1.0
KAPPA
the force constant for the wall
=20000
OFFSET
the offset for the start of the wall
=0 restr_rmsd:
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
ARG
the arguments on which the bias is acting
=rmsd
AT
the positions of the wall
=0.10
KAPPA
the force constant for the wall
=20000
OFFSET
the offset for the start of the wall
=0
# Coordination number c:
COORDINATION
Calculate coordination numbers. More details
GROUPA
First list of atoms
=AR6
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,siga,theta
GRID_MIN
the lower bounds for the grid
=0,0,-pi
GRID_MAX
the upper bounds for the grid
=3.6,1.2,pi
SIGMA
the widths of the Gaussian hills
=0.1,0.04,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
=298
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
=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
=5000
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_rho.*,restr_siga.*,restr_rmsd
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
=5000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=ref_coord.x,ref_coord.y,ref_coord.z
FILE
the name of the file on which to output these quantities
=ref_coord.dat
STRIDE
the frequency with which the quantities of interest should be output
=5000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=AR6_coord.x,AR6_coord.y,AR6_coord.z
FILE
the name of the file on which to output these quantities
=AR6_coord.dat
STRIDE
the frequency with which the quantities of interest should be output
=5000
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,siga,theta
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
=5000
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
=5000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=rmsd
FILE
the name of the file on which to output these quantities
=rmsd.dat
STRIDE
the frequency with which the quantities of interest should be output
=5000
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=Dis
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
=5000
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
=5000