PLUMED-NEST-TEST-SITE

Project ID: plumID:25.005
Source: dimer_octahedral/plumed.dat
Originally used with PLUMED version: 2.8.2
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A ENERGYthe units of energy=kcal/mol TIMEthe units of time=fs
The UNITS action with label  calculates somethingFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1

# define groups of different atoms
AG: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-3,12-14
The GROUP action with label AG calculates somethingS: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=4-6,15-17
The GROUP action with label S calculates somethingC: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=10,11,21-24
The GROUP action with label C calculates somethingN: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=7-9,18-20
The GROUP action with label N calculates somethingH: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=25-36
The GROUP action with label H calculates somethingO_S: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=41-726:6

# define center of mass of Ag atoms
The GROUP action with label O_S calculates somethingc: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-3,12-14

# define fixed atom near center of the box
The COM action with label c calculates somethingc_box: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=10.63933,9.75917,9.83800

# distance between COM of Ag atoms and center of the box
The FIXEDATOM action with label c_box calculates somethingd: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c,c_box

# define coordination numbers for Ag and S atoms
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
the DISTANCE between this pair of atomscn_s1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=16 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=14 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8 
The COORDINATION action with label cn_s1 calculates the following quantities:
 Quantity   
 Description  
cn_s1.value
the value of the coordinationcn_s2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1  R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
The COORDINATION action with label cn_s2 calculates the following quantities:
 Quantity   
 Description  
cn_s2.value
the value of the coordinationcn_s3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2  R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
The COORDINATION action with label cn_s3 calculates the following quantities:
 Quantity   
 Description  
cn_s3.value
the value of the coordinationcn_s4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=17 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3  R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
The COORDINATION action with label cn_s4 calculates the following quantities:
 Quantity   
 Description  
cn_s4.value
the value of the coordinationcn_s5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=12 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
The COORDINATION action with label cn_s5 calculates the following quantities:
 Quantity   
 Description  
cn_s5.value
the value of the coordinationcn_s6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=15 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=13 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
The COORDINATION action with label cn_s6 calculates the following quantities:
 Quantity   
 Description  
cn_s6.value
the value of the coordinationcn_ag_box: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=AG GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=c_box R_0The r_0 parameter of the switching function=3.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8

# CV2 solvent coordination around center of the box
The COORDINATION action with label cn_ag_box calculates the following quantities:
 Quantity   
 Description  
cn_ag_box.value
the value of the coordinationcn: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=c_box GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O_S R_0The r_0 parameter of the switching function=3.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10

# CV1 solute coordination
The COORDINATION action with label cn calculates the following quantities:
 Quantity   
 Description  
cn.value
the value of the coordinations1: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn_ag_box,cn_s1,cn_s2,cn_s3,cn_s4,cn_s5,cn_s6 COEFFICIENTS the coefficients of the arguments in your function=1,1,1,1,1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# WT-Metad block
The COMBINE action with label s1 calculates the following quantities:
 Quantity   
 Description  
s1.value
a linear compbinationmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=s1,cn PACEthe frequency for hill addition=100 FILE a file in which the list of added hills is stored=HILLS TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=15 SIGMAthe widths of the Gaussian hills=0.1,0.025 HEIGHTthe heights of the Gaussian hills=2

# define lowest coordination of different atoms to monitor ML potential stability
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialcn_H: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=25-36,42-726:6,38-726:6,39-726:6,40-726:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-726 R_0The r_0 parameter of the switching function=1.2 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The COORDINATIONNUMBER action with label cn_H calculates the following quantities:
 Quantity   
 Description  
cn_H.lowest
the smallest of the colvars
cn_H.value
the coordination numbers of the specified atomscn_CH3: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=37-726:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=42-726:6,38-726:6,39-726:6,40-726:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
The COORDINATIONNUMBER action with label cn_CH3 calculates the following quantities:
 Quantity   
 Description  
cn_CH3.lowest
the smallest of the colvars
cn_CH3.value
the coordination numbers of the specified atomscn_CO: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=41-726:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=37-726:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility

# define minimum distance between all hydrogen atoms
The COORDINATIONNUMBER action with label cn_CO calculates the following quantities:
 Quantity   
 Description  
cn_CO.lowest
the smallest of the colvars
cn_CO.value
the coordination numbers of the specified atomsHgrp: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=25-36,42-726:6,38-726:6,39-726:6,40-726:6
The GROUP action with label Hgrp calculates somethingdHH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hgrp GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hgrp MINcalculate the minimum value={BETA=20} NOPBC ignore the periodic boundary conditions when calculating distances

# define wall for S and non bonding Ag
The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum colvar
dHH.value
the DISTANCES between the each pair of atoms that were specifiedS1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=16 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2,3,12,13  R_0The r_0 parameter of the switching function=2.75
The COORDINATION action with label S1 calculates the following quantities:
 Quantity   
 Description  
S1.value
the value of the coordinationS2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3,12,13,14 R_0The r_0 parameter of the switching function=2.75
The COORDINATION action with label S2 calculates the following quantities:
 Quantity   
 Description  
S2.value
the value of the coordinationS3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=6  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,3,12,13  R_0The r_0 parameter of the switching function=2.75
The COORDINATION action with label S3 calculates the following quantities:
 Quantity   
 Description  
S3.value
the value of the coordinationS4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=17 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,2,12,14  R_0The r_0 parameter of the switching function=2.75
The COORDINATION action with label S4 calculates the following quantities:
 Quantity   
 Description  
S4.value
the value of the coordinationS5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,2,13,14  R_0The r_0 parameter of the switching function=2.75
The COORDINATION action with label S5 calculates the following quantities:
 Quantity   
 Description  
S5.value
the value of the coordinationS6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=15 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,2,3,14   R_0The r_0 parameter of the switching function=2.75

# define walls to keep system in the region of interest
The COORDINATION action with label S6 calculates the following quantities:
 Quantity   
 Description  
S6.value
the value of the coordinationa1: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,13,727
The ANGLE action with label a1 calculates the following quantities:
 Quantity   
 Description  
a1.value
the ANGLE involving these atomsa2: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=12,14,727
The ANGLE action with label a2 calculates the following quantities:
 Quantity   
 Description  
a2.value
the ANGLE involving these atomsa3: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=2,3,727

The ANGLE action with label a3 calculates the following quantities:
 Quantity   
 Description  
a3.value
the ANGLE involving these atomsa4: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,727,12
The ANGLE action with label a4 calculates the following quantities:
 Quantity   
 Description  
a4.value
the ANGLE involving these atomsa5: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=2,727,13
The ANGLE action with label a5 calculates the following quantities:
 Quantity   
 Description  
a5.value
the ANGLE involving these atomsa6: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=3,727,14

The ANGLE action with label a6 calculates the following quantities:
 Quantity   
 Description  
a6.value
the ANGLE involving these atomsd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,3
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,12
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,13
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,14

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd1cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,4
The DISTANCE action with label d1cs calculates the following quantities:
 Quantity   
 Description  
d1cs.value
the DISTANCE between this pair of atomsd2cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,5
The DISTANCE action with label d2cs calculates the following quantities:
 Quantity   
 Description  
d2cs.value
the DISTANCE between this pair of atomsd3cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,6
The DISTANCE action with label d3cs calculates the following quantities:
 Quantity   
 Description  
d3cs.value
the DISTANCE between this pair of atomsd4cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,15
The DISTANCE action with label d4cs calculates the following quantities:
 Quantity   
 Description  
d4cs.value
the DISTANCE between this pair of atomsd5cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,16
The DISTANCE action with label d5cs calculates the following quantities:
 Quantity   
 Description  
d5cs.value
the DISTANCE between this pair of atomsd6cs: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,17

The DISTANCE action with label d6cs calculates the following quantities:
 Quantity   
 Description  
d6cs.value
the DISTANCE between this pair of atomsd1cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,7
The DISTANCE action with label d1cn calculates the following quantities:
 Quantity   
 Description  
d1cn.value
the DISTANCE between this pair of atomsd2cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,8
The DISTANCE action with label d2cn calculates the following quantities:
 Quantity   
 Description  
d2cn.value
the DISTANCE between this pair of atomsd3cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,9
The DISTANCE action with label d3cn calculates the following quantities:
 Quantity   
 Description  
d3cn.value
the DISTANCE between this pair of atomsd4cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,18
The DISTANCE action with label d4cn calculates the following quantities:
 Quantity   
 Description  
d4cn.value
the DISTANCE between this pair of atomsd5cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,19
The DISTANCE action with label d5cn calculates the following quantities:
 Quantity   
 Description  
d5cn.value
the DISTANCE between this pair of atomsd6cn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,20

The DISTANCE action with label d6cn calculates the following quantities:
 Quantity   
 Description  
d6cn.value
the DISTANCE between this pair of atomsd1n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=20,1
The DISTANCE action with label d1n calculates the following quantities:
 Quantity   
 Description  
d1n.value
the DISTANCE between this pair of atomsd2n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,2
The DISTANCE action with label d2n calculates the following quantities:
 Quantity   
 Description  
d2n.value
the DISTANCE between this pair of atomsd3n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=8,3
The DISTANCE action with label d3n calculates the following quantities:
 Quantity   
 Description  
d3n.value
the DISTANCE between this pair of atomsd4n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,12
The DISTANCE action with label d4n calculates the following quantities:
 Quantity   
 Description  
d4n.value
the DISTANCE between this pair of atomsd5n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=18,13
The DISTANCE action with label d5n calculates the following quantities:
 Quantity   
 Description  
d5n.value
the DISTANCE between this pair of atomsd6n: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=19,14

The DISTANCE action with label d6n calculates the following quantities:
 Quantity   
 Description  
d6n.value
the DISTANCE between this pair of atomsd1s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,1
The DISTANCE action with label d1s calculates the following quantities:
 Quantity   
 Description  
d1s.value
the DISTANCE between this pair of atomsd2s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,2
The DISTANCE action with label d2s calculates the following quantities:
 Quantity   
 Description  
d2s.value
the DISTANCE between this pair of atomsd3s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,3
The DISTANCE action with label d3s calculates the following quantities:
 Quantity   
 Description  
d3s.value
the DISTANCE between this pair of atomsd4s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,12
The DISTANCE action with label d4s calculates the following quantities:
 Quantity   
 Description  
d4s.value
the DISTANCE between this pair of atomsd5s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,13
The DISTANCE action with label d5s calculates the following quantities:
 Quantity   
 Description  
d5s.value
the DISTANCE between this pair of atomsd6s: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,14

The DISTANCE action with label d6s calculates the following quantities:
 Quantity   
 Description  
d6s.value
the DISTANCE between this pair of atomsuwall_s_ag: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=S1,S2,S3,S4,S5,S6 ATthe positions of the wall=0.5,0.5,0.5,0.5,0.5,0.5 KAPPAthe force constant for the wall=100,100,100,100,100,100

The UPPER_WALLS action with label uwall_s_ag calculates the following quantities:
 Quantity   
 Description  
uwall_s_ag.bias
the instantaneous value of the bias potential
uwall_s_ag.force2
the instantaneous value of the squared force due to this bias potentialuwall_a: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1,a2,a3 ATthe positions of the wall=1.5,1.5,1.5 KAPPAthe force constant for the wall=100,100,100
The UPPER_WALLS action with label uwall_a calculates the following quantities:
 Quantity   
 Description  
uwall_a.bias
the instantaneous value of the bias potential
uwall_a.force2
the instantaneous value of the squared force due to this bias potentiallwall_a: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1,a2,a3 ATthe positions of the wall=0.65,0.65,0.65 KAPPAthe force constant for the wall=100,100,100
The LOWER_WALLS action with label lwall_a calculates the following quantities:
 Quantity   
 Description  
lwall_a.bias
the instantaneous value of the bias potential
lwall_a.force2
the instantaneous value of the squared force due to this bias potentiallwall_a2: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a4,a5,a6 ATthe positions of the wall=2.4,2.4,2.4 KAPPAthe force constant for the wall=100,100,100

The LOWER_WALLS action with label lwall_a2 calculates the following quantities:
 Quantity   
 Description  
lwall_a2.bias
the instantaneous value of the bias potential
lwall_a2.force2
the instantaneous value of the squared force due to this bias potentiallwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5,d6 ATthe positions of the wall=1.5,1.5,1.5,1.5,1.5,1.5 KAPPAthe force constant for the wall=100,100,100,100,100,100
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4,d5,d6 ATthe positions of the wall=5,5,5,5,5,5 KAPPAthe force constant for the wall=100,100,100,100,100,100

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentiallwallcn: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1cn,d2cn,d3cn,d4cn,d5cn,d6cn ATthe positions of the wall=3,3,3,3,3,3 KAPPAthe force constant for the wall=100,100,100,100,100,100
The LOWER_WALLS action with label lwallcn calculates the following quantities:
 Quantity   
 Description  
lwallcn.bias
the instantaneous value of the bias potential
lwallcn.force2
the instantaneous value of the squared force due to this bias potentiallwallcs: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1cs,d2cs,d3cs,d4cs,d5cs,d6cs ATthe positions of the wall=3,3,3,3,3,3 KAPPAthe force constant for the wall=100,100,100,100,100,100

The LOWER_WALLS action with label lwallcs calculates the following quantities:
 Quantity   
 Description  
lwallcs.bias
the instantaneous value of the bias potential
lwallcs.force2
the instantaneous value of the squared force due to this bias potentialuwalln: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1n,d2n,d3n,d4n,d5n,d6n ATthe positions of the wall=2.7,2.7,2.7,2.7,2.7,2.7 KAPPAthe force constant for the wall=100,100,100,100,100,100
The UPPER_WALLS action with label uwalln calculates the following quantities:
 Quantity   
 Description  
uwalln.bias
the instantaneous value of the bias potential
uwalln.force2
the instantaneous value of the squared force due to this bias potentialuwalls: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1s,d2s,d3s,d4s,d5s,d6s ATthe positions of the wall=2.7,2.7,2.7,2.7,2.7,2.7 KAPPAthe force constant for the wall=100,100,100,100,100,100

The UPPER_WALLS action with label uwalls calculates the following quantities:
 Quantity   
 Description  
uwalls.bias
the instantaneous value of the bias potential
uwalls.force2
the instantaneous value of the squared force due to this bias potentialuwall_cn: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cn ATthe positions of the wall=5.0 KAPPAthe force constant for the wall=100
The UPPER_WALLS action with label uwall_cn calculates the following quantities:
 Quantity   
 Description  
uwall_cn.bias
the instantaneous value of the bias potential
uwall_cn.force2
the instantaneous value of the squared force due to this bias potentialcn_wall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cn_CH3.lowest,cn_CO.lowest ATthe positions of the wall=2.55,0.47 KAPPAthe force constant for the wall=100,100

The LOWER_WALLS action with label cn_wall calculates the following quantities:
 Quantity   
 Description  
cn_wall.bias
the instantaneous value of the bias potential
cn_wall.force2
the instantaneous value of the squared force due to this bias potentialres: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=d ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100

# define print statement
The RESTRAINT action with label res calculates the following quantities:
 Quantity   
 Description  
res.bias
the instantaneous value of the bias potential
res.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=colvar ARGthe labels of the values that you would like to print to the file=*