PLUMED-NEST

Project ID: plumID:23.037
Source: SBP_plumed_nest/Plumed_files/K8AK11A/plumed.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

#RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=K8AK11A_ACE_NME.pdb


# com: COM ATOMS=9025-9207
The MOLINFO action with label  calculates somethingncap: 
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
=9025-9030
The COM action with label ncap calculates somethingccap: 
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
=9202-9207

The COM action with label ccap calculates somethingbb: 
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
=9029,9030,9031,9033,9041,9042,9043,9045,9052,9053,9054,9056,9062,9063,9064,9066,9086,9087,9088,9090,9093,9094,9095,9097,9113,9114,9115,9117,9135,9136,9137,9139,9145,9146,9147,9151,9159,9160,9161,9163,9166,9167,9168,9170,9176,9177,9178,9180,9200,9201,9202,9204

The COM action with label bb calculates somethingasp: 
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
=9035-9040
The COM action with label asp calculates somethingser: 
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
=9047-9051
The COM action with label ser calculates somethingala: 
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
=9058-9061
The COM action with label ala calculates somethingarg: 
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
=9068-9085
The COM action with label arg calculates somethinggly: 
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
=9090-9092
The COM action with label gly calculates somethingphe: 
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
=9099-9112
The COM action with label phe calculates somethinglys: 
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
=9119-9134
The COM action with label lys calculates somethingala2: 
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
=9141-9144
The COM action with label ala2 calculates somethingpro: 
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
=9153-9158
The COM action with label pro calculates somethinggly2: 
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
=9163-9165
The COM action with label gly2 calculates somethingala3: 
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
=9172-9175
The COM action with label ala3 calculates somethingarg2: 
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
=9182-9199

The COM action with label arg2 calculates somethingtop_oh: 
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
=38,49,52,54,56,59,62,65,67,69,72,74,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,2294,2305,2308,2310,2312,2315,2318,2321,2323,2325,2328,2330,2392,2393,2394,2395,2396,2397,2398,2399,2400,2401,2402,2403,2404,2405,2406,2407,2408,2409,2410,2411,2412,2413,2414,2415,2416,2417,2418,2419,2420,2421,2422,2423,2424,2425,2426,2427,2428,2429,2430,2431,2432,2433,2434,2435,2436,2437,2438,2439,2440,2441,2442,2443,2444,2445,2446,2447,4550,4561,4564,4566,4568,4571,4574,4577,4579,4581,4584,4586,4648,4649,4650,4651,4652,4653,4654,4655,4656,4657,4658,4659,4660,4661,4662,4663,4664,4665,4666,4667,4668,4669,4670,4671,4672,4673,4674,4675,4676,4677,4678,4679,4680,4681,4682,4683,4684,4685,4686,4687,4688,4689,4690,4691,4692,4693,4694,4695,4696,4697,4698,4699,4700,4701,4702,4703,6806,6817,6820,6822,6824,6827,6830,6833,6835,6837,6840,6842,6904,6905,6906,6907,6908,6909,6910,6911,6912,6913,6914,6915,6916,6917,6918,6919,6920,6921,6922,6923,6924,6925,6926,6927,6928,6929,6930,6931,6932,6933,6934,6935,6936,6937,6938,6939,6940,6941,6942,6943,6944,6945,6946,6947,6948,6949,6950,6951,6952,6953,6954,6955,6956,6957,6958,6959

The COM action with label top_oh calculates somethingdcaps: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ncap,ccap
The DISTANCE action with label dcaps calculates the following quantities:
 Quantity   
 Description  
dcaps.value
the DISTANCE between this pair of atomsdncap: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ncap 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dncap calculates the following quantities:
 Quantity   
 Description  
dncap.x
the x-component of the vector connecting the two atoms
dncap.y
the y-component of the vector connecting the two atoms
dncap.z
the z-component of the vector connecting the two atoms
dncap.value
the DISTANCE between this pair of atomsdccap: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ccap 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
# dcom: DISTANCE ATOMS=top_oh,com COMPONENTS NOPBC

The DISTANCE action with label dccap calculates the following quantities:
 Quantity   
 Description  
dccap.x
the x-component of the vector connecting the two atoms
dccap.y
the y-component of the vector connecting the two atoms
dccap.z
the z-component of the vector connecting the two atoms
dccap.value
the DISTANCE between this pair of atomsdbb: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,bb 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dbb calculates the following quantities:
 Quantity   
 Description  
dbb.x
the x-component of the vector connecting the two atoms
dbb.y
the y-component of the vector connecting the two atoms
dbb.z
the z-component of the vector connecting the two atoms
dbb.value
the DISTANCE between this pair of atomsdasp: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,asp 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dasp calculates the following quantities:
 Quantity   
 Description  
dasp.x
the x-component of the vector connecting the two atoms
dasp.y
the y-component of the vector connecting the two atoms
dasp.z
the z-component of the vector connecting the two atoms
dasp.value
the DISTANCE between this pair of atomsdser: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ser 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dser calculates the following quantities:
 Quantity   
 Description  
dser.x
the x-component of the vector connecting the two atoms
dser.y
the y-component of the vector connecting the two atoms
dser.z
the z-component of the vector connecting the two atoms
dser.value
the DISTANCE between this pair of atomsdala: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ala 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dala calculates the following quantities:
 Quantity   
 Description  
dala.x
the x-component of the vector connecting the two atoms
dala.y
the y-component of the vector connecting the two atoms
dala.z
the z-component of the vector connecting the two atoms
dala.value
the DISTANCE between this pair of atomsdarg: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,arg 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label darg calculates the following quantities:
 Quantity   
 Description  
darg.x
the x-component of the vector connecting the two atoms
darg.y
the y-component of the vector connecting the two atoms
darg.z
the z-component of the vector connecting the two atoms
darg.value
the DISTANCE between this pair of atomsdgly: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,gly 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dgly calculates the following quantities:
 Quantity   
 Description  
dgly.x
the x-component of the vector connecting the two atoms
dgly.y
the y-component of the vector connecting the two atoms
dgly.z
the z-component of the vector connecting the two atoms
dgly.value
the DISTANCE between this pair of atomsdphe: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,phe 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dphe calculates the following quantities:
 Quantity   
 Description  
dphe.x
the x-component of the vector connecting the two atoms
dphe.y
the y-component of the vector connecting the two atoms
dphe.z
the z-component of the vector connecting the two atoms
dphe.value
the DISTANCE between this pair of atomsdlys: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,lys 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dlys calculates the following quantities:
 Quantity   
 Description  
dlys.x
the x-component of the vector connecting the two atoms
dlys.y
the y-component of the vector connecting the two atoms
dlys.z
the z-component of the vector connecting the two atoms
dlys.value
the DISTANCE between this pair of atomsdala2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ala2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dala2 calculates the following quantities:
 Quantity   
 Description  
dala2.x
the x-component of the vector connecting the two atoms
dala2.y
the y-component of the vector connecting the two atoms
dala2.z
the z-component of the vector connecting the two atoms
dala2.value
the DISTANCE between this pair of atomsdpro: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,pro 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dpro calculates the following quantities:
 Quantity   
 Description  
dpro.x
the x-component of the vector connecting the two atoms
dpro.y
the y-component of the vector connecting the two atoms
dpro.z
the z-component of the vector connecting the two atoms
dpro.value
the DISTANCE between this pair of atomsdgly2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,gly2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dgly2 calculates the following quantities:
 Quantity   
 Description  
dgly2.x
the x-component of the vector connecting the two atoms
dgly2.y
the y-component of the vector connecting the two atoms
dgly2.z
the z-component of the vector connecting the two atoms
dgly2.value
the DISTANCE between this pair of atomsdala3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,ala3 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label dala3 calculates the following quantities:
 Quantity   
 Description  
dala3.x
the x-component of the vector connecting the two atoms
dala3.y
the y-component of the vector connecting the two atoms
dala3.z
the z-component of the vector connecting the two atoms
dala3.value
the DISTANCE between this pair of atomsdarg2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=top_oh,arg2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# UPPER_WALLS ARG=dcom.z AT=5.5 KAPPA=1000000 LABEL=uwall_dcom
The DISTANCE action with label darg2 calculates the following quantities:
 Quantity   
 Description  
darg2.x
the x-component of the vector connecting the two atoms
darg2.y
the y-component of the vector connecting the two atoms
darg2.z
the z-component of the vector connecting the two atoms
darg2.value
the DISTANCE between this pair of atoms
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dcaps 
AT
the positions of the wall
=0.8 
KAPPA
the force constant for the wall
=100000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dcaps_min
The LOWER_WALLS action with label dcaps_min calculates something
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
=dcaps 
AT
the positions of the wall
=1.2 
KAPPA
the force constant for the wall
=100000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dcaps_max
The UPPER_WALLS action with label dcaps_max calculates something
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dncap.z 
AT
the positions of the wall
=0.7 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dncap_min
The LOWER_WALLS action with label dncap_min calculates something
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dccap.z 
AT
the positions of the wall
=0.7 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dccap_min

The LOWER_WALLS action with label dccap_min calculates something
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
=dbb.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dbb
The UPPER_WALLS action with label uwall_dbb calculates something
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
=dasp.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dasp
The UPPER_WALLS action with label uwall_dasp calculates something
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
=dser.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dser
The UPPER_WALLS action with label uwall_dser calculates something
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
=dala.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dala
The UPPER_WALLS action with label uwall_dala calculates something
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
=darg.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_darg
The UPPER_WALLS action with label uwall_darg calculates something
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
=dgly.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dgly
The UPPER_WALLS action with label uwall_dgly calculates something
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
=dphe.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dphe
The UPPER_WALLS action with label uwall_dphe calculates something
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
=dlys.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dlys
The UPPER_WALLS action with label uwall_dlys calculates something
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
=dala2.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dala2
The UPPER_WALLS action with label uwall_dala2 calculates something
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
=dpro.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dpro
The UPPER_WALLS action with label uwall_dpro calculates something
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
=dgly2.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dgly2
The UPPER_WALLS action with label uwall_dgly2 calculates something
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
=dala3.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_dala3
The UPPER_WALLS action with label uwall_dala3 calculates something
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
=darg2.z 
AT
the positions of the wall
=6.5 
KAPPA
the force constant for the wall
=1000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_darg2

The UPPER_WALLS action with label uwall_darg2 calculates something
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=9025-9207 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg

The GYRATION action with label rg calculates something
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
ARG
the input for this action is the scalar output from one or more other actions
=dbb.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dala2.z,dpro.z,dgly2.z,dala3.z,darg2.z,rg
SIGMA
the widths of the Gaussian hills
=200.0
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2 #kJ/mol
PACE
the frequency for hill addition, one for all biases
=500
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=30  # Sqrt[cv]*8
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=PBMETAD
GRID_MIN
the lower bounds for the grid
=-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,-0.5,0.0
GRID_MAX
the upper bounds for the grid
=7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0,7.0
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=../HILLS.dbb,../HILLS.dasp,../HILLS.dser,../HILLS.dala,../HILLS.darg,../HILLS.dgly,../HILLS.dphe,../HILLS.dlys,../HILLS.dala2,../HILLS.dpro,../HILLS.dgly2,../HILLS.dala3,../HILLS.darg2,../HILLS.rg
... PBMETAD

The PBMETAD action with label PBMETAD calculates the following quantities:
 Quantity   
 Description  
PBMETAD.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=PBMETAD.bias,dcaps,dbb.z,dncap.z,dccap.z,dasp.z,dser.z,dala.z,darg.z,dgly.z,dphe.z,dlys.z,dala2.z,dpro.z,dgly2.z,dala3.z,darg2.z,rg 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR