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
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
AGThe GROUP action with label AG calculates the following quantities:| Quantity | Type | Description |
| AG | atoms | indices of atoms specified in GROUP |
: 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
SThe GROUP action with label S calculates the following quantities:| Quantity | Type | Description |
| S | atoms | indices of atoms specified in GROUP |
: 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
CThe GROUP action with label C calculates the following quantities:| Quantity | Type | Description |
| C | atoms | indices of atoms specified in GROUP |
: 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
NThe GROUP action with label N calculates the following quantities:| Quantity | Type | Description |
| N | atoms | indices of atoms specified in GROUP |
: 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
HThe GROUP action with label H calculates the following quantities:| Quantity | Type | Description |
| H | atoms | indices of atoms specified in GROUP |
: 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
O_SThe GROUP action with label O_S calculates the following quantities:| Quantity | Type | Description |
| O_S | atoms | indices of atoms specified in GROUP |
: 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
cThe COM action with label c calculates the following quantities:| Quantity | Type | Description |
| c | atoms | virtual atom calculated by COM action |
: 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
c_boxThe FIXEDATOM action with label c_box calculates the following quantities:| Quantity | Type | Description |
| c_box | atoms | virtual atom calculated by FIXEDATOM action |
: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=10.63933,9.75917,9.83800
c_box: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=10.63933,9.75917,9.83800 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
dThe DISTANCE action with label d calculates the following quantities:| Quantity | Type | Description |
| d | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c,c_box
cn_s1The COORDINATION action with label cn_s1 calculates the following quantities:| Quantity | Type | Description |
| cn_s1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_s2The COORDINATION action with label cn_s2 calculates the following quantities:| Quantity | Type | Description |
| cn_s2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_s3The COORDINATION action with label cn_s3 calculates the following quantities:| Quantity | Type | Description |
| cn_s3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_s4The COORDINATION action with label cn_s4 calculates the following quantities:| Quantity | Type | Description |
| cn_s4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_s5The COORDINATION action with label cn_s5 calculates the following quantities:| Quantity | Type | Description |
| cn_s5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_s6The COORDINATION action with label cn_s6 calculates the following quantities:| Quantity | Type | Description |
| cn_s6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_s6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cn_ag_boxThe COORDINATION action with label cn_ag_box calculates the following quantities:| Quantity | Type | Description |
| cn_ag_box | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn_ag_box: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
cnThe COORDINATION action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
cn: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0
s1The COMBINE action with label s1 calculates the following quantities:| Quantity | Type | Description |
| s1 | scalar | a linear compbination |
: 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
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
: 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
cn_HThe COORDINATIONNUMBER action with label cn_H calculates the following quantities:| Quantity | Type | Description |
| cn_H | vector | the coordination numbers of the specified atoms |
| cn_H_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. 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
cn_H: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_H: COORDINATIONNUMBER SPECIESA=25-36,42-726:6,38-726:6,39-726:6,40-726:6 SPECIESB=1-726 R_0=1.2 LOWEST LOWMEM
cn_H_grpThe GROUP action with label cn_H_grp calculates the following quantities:| Quantity | Type | Description |
| cn_H_grp | atoms | indices of atoms specified in GROUP |
: 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
cn_H_matThe CONTACT_MATRIX action with label cn_H_mat calculates the following quantities:| Quantity | Type | Description |
| cn_H_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=25-36,42-726:6,38-726:6,39-726:6,40-726:6 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=1-726 R_0The r_0 parameter of the switching function=1.2 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_H_onesThe CONSTANT action with label cn_H_ones calculates the following quantities:| Quantity | Type | Description |
| cn_H_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=726
cn_HThe MATRIX_VECTOR_PRODUCT action with label cn_H calculates the following quantities:| Quantity | Type | Description |
| cn_H | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cn_H_mat,cn_H_ones
cn_H_caverageThe MEAN action with label cn_H_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_H_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn_H PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_H_lowestThe LOWEST action with label cn_H_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_H_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_H
# --- End of included input --- cn_CH3The COORDINATIONNUMBER action with label cn_CH3 calculates the following quantities:| Quantity | Type | Description |
| cn_CH3 | vector | the coordination numbers of the specified atoms |
| cn_CH3_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. 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
cn_CH3: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_CH3: COORDINATIONNUMBER SPECIESA=37-726:6 SPECIESB=42-726:6,38-726:6,39-726:6,40-726:6 R_0=1.5 LOWEST LOWMEM
cn_CH3_grpThe GROUP action with label cn_CH3_grp calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_grp | atoms | indices of atoms specified in GROUP |
: 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=37-726:6
cn_CH3_matThe CONTACT_MATRIX action with label cn_CH3_mat calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=37-726:6 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=42-726:6,38-726:6,39-726:6,40-726:6 R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_CH3_onesThe CONSTANT action with label cn_CH3_ones calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=460
cn_CH3The MATRIX_VECTOR_PRODUCT action with label cn_CH3 calculates the following quantities:| Quantity | Type | Description |
| cn_CH3 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cn_CH3_mat,cn_CH3_ones
cn_CH3_caverageThe MEAN action with label cn_CH3_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn_CH3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_CH3_lowestThe LOWEST action with label cn_CH3_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_CH3
# --- End of included input --- cn_COThe COORDINATIONNUMBER action with label cn_CO calculates the following quantities:| Quantity | Type | Description |
| cn_CO | vector | the coordination numbers of the specified atoms |
| cn_CO_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. 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
cn_CO: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_CO: COORDINATIONNUMBER SPECIESA=41-726:6 SPECIESB=37-726:6 R_0=1.5 LOWEST LOWMEM
cn_CO_grpThe GROUP action with label cn_CO_grp calculates the following quantities:| Quantity | Type | Description |
| cn_CO_grp | atoms | indices of atoms specified in GROUP |
: 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
cn_CO_matThe CONTACT_MATRIX action with label cn_CO_mat calculates the following quantities:| Quantity | Type | Description |
| cn_CO_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=41-726:6 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=37-726:6 R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_CO_onesThe CONSTANT action with label cn_CO_ones calculates the following quantities:| Quantity | Type | Description |
| cn_CO_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=115
cn_COThe MATRIX_VECTOR_PRODUCT action with label cn_CO calculates the following quantities:| Quantity | Type | Description |
| cn_CO | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cn_CO_mat,cn_CO_ones
cn_CO_caverageThe MEAN action with label cn_CO_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_CO_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn_CO PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_CO_lowestThe LOWEST action with label cn_CO_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_CO_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_CO
# --- End of included input ---
HgrpThe GROUP action with label Hgrp calculates the following quantities:| Quantity | Type | Description |
| Hgrp | atoms | indices of atoms specified in GROUP |
: 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
dHHThe DISTANCES action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCES between the each pair of atoms that were specified |
| dHH_min | scalar | the minimum colvar |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. 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
# dHH: DISTANCES GROUPA=Hgrp GROUPB=Hgrp MIN={BETA=20} NOPBC
dHHThe DISTANCE action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=25,25 ATOMS2the pair of atom that we are calculating the distance between=25,26 ATOMS3the pair of atom that we are calculating the distance between=25,27 ATOMS4the pair of atom that we are calculating the distance between=25,28 ATOMS5the pair of atom that we are calculating the distance between=25,29
dHH_me_minThe CUSTOM action with label dHH_me_min calculates the following quantities:| Quantity | Type | Description |
| dHH_me_min | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHH FUNCthe function you wish to evaluate=exp(20/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHH_mec_minThe SUM action with label dHH_mec_min calculates the following quantities:| Quantity | Type | Description |
| dHH_mec_min | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dHH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHH_minThe CUSTOM action with label dHH_min calculates the following quantities:| Quantity | Type | Description |
| dHH_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHH_mec_min FUNCthe function you wish to evaluate=20/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
S1The COORDINATION action with label S1 calculates the following quantities:| Quantity | Type | Description |
| S1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
S2The COORDINATION action with label S2 calculates the following quantities:| Quantity | Type | Description |
| S2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
S3The COORDINATION action with label S3 calculates the following quantities:| Quantity | Type | Description |
| S3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
S4The COORDINATION action with label S4 calculates the following quantities:| Quantity | Type | Description |
| S4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
S5The COORDINATION action with label S5 calculates the following quantities:| Quantity | Type | Description |
| S5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
S6The COORDINATION action with label S6 calculates the following quantities:| Quantity | Type | Description |
| S6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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
S6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
a1The ANGLE action with label a1 calculates the following quantities:| Quantity | Type | Description |
| a1 | scalar | the ANGLE involving these atoms |
: 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
a2The ANGLE action with label a2 calculates the following quantities:| Quantity | Type | Description |
| a2 | scalar | the ANGLE involving these atoms |
: 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
a3The ANGLE action with label a3 calculates the following quantities:| Quantity | Type | Description |
| a3 | scalar | the ANGLE involving these atoms |
: 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
a4The ANGLE action with label a4 calculates the following quantities:| Quantity | Type | Description |
| a4 | scalar | the ANGLE involving these atoms |
: 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
a5The ANGLE action with label a5 calculates the following quantities:| Quantity | Type | Description |
| a5 | scalar | the ANGLE involving these atoms |
: 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
a6The ANGLE action with label a6 calculates the following quantities:| Quantity | Type | Description |
| a6 | scalar | the ANGLE involving these atoms |
: 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
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,1
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,2
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,3
d4The DISTANCE action with label d4 calculates the following quantities:| Quantity | Type | Description |
| d4 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,12
d5The DISTANCE action with label d5 calculates the following quantities:| Quantity | Type | Description |
| d5 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,13
d6The DISTANCE action with label d6 calculates the following quantities:| Quantity | Type | Description |
| d6 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,14
d1csThe DISTANCE action with label d1cs calculates the following quantities:| Quantity | Type | Description |
| d1cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,4
d2csThe DISTANCE action with label d2cs calculates the following quantities:| Quantity | Type | Description |
| d2cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,5
d3csThe DISTANCE action with label d3cs calculates the following quantities:| Quantity | Type | Description |
| d3cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,6
d4csThe DISTANCE action with label d4cs calculates the following quantities:| Quantity | Type | Description |
| d4cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,15
d5csThe DISTANCE action with label d5cs calculates the following quantities:| Quantity | Type | Description |
| d5cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,16
d6csThe DISTANCE action with label d6cs calculates the following quantities:| Quantity | Type | Description |
| d6cs | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,17
d1cnThe DISTANCE action with label d1cn calculates the following quantities:| Quantity | Type | Description |
| d1cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,7
d2cnThe DISTANCE action with label d2cn calculates the following quantities:| Quantity | Type | Description |
| d2cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,8
d3cnThe DISTANCE action with label d3cn calculates the following quantities:| Quantity | Type | Description |
| d3cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,9
d4cnThe DISTANCE action with label d4cn calculates the following quantities:| Quantity | Type | Description |
| d4cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,18
d5cnThe DISTANCE action with label d5cn calculates the following quantities:| Quantity | Type | Description |
| d5cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,19
d6cnThe DISTANCE action with label d6cn calculates the following quantities:| Quantity | Type | Description |
| d6cn | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,20
d1nThe DISTANCE action with label d1n calculates the following quantities:| Quantity | Type | Description |
| d1n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=20,1
d2nThe DISTANCE action with label d2n calculates the following quantities:| Quantity | Type | Description |
| d2n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,2
d3nThe DISTANCE action with label d3n calculates the following quantities:| Quantity | Type | Description |
| d3n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=8,3
d4nThe DISTANCE action with label d4n calculates the following quantities:| Quantity | Type | Description |
| d4n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,12
d5nThe DISTANCE action with label d5n calculates the following quantities:| Quantity | Type | Description |
| d5n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=18,13
d6nThe DISTANCE action with label d6n calculates the following quantities:| Quantity | Type | Description |
| d6n | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=19,14
d1sThe DISTANCE action with label d1s calculates the following quantities:| Quantity | Type | Description |
| d1s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,1
d2sThe DISTANCE action with label d2s calculates the following quantities:| Quantity | Type | Description |
| d2s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,2
d3sThe DISTANCE action with label d3s calculates the following quantities:| Quantity | Type | Description |
| d3s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,3
d4sThe DISTANCE action with label d4s calculates the following quantities:| Quantity | Type | Description |
| d4s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,12
d5sThe DISTANCE action with label d5s calculates the following quantities:| Quantity | Type | Description |
| d5s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,13
d6sThe DISTANCE action with label d6s calculates the following quantities:| Quantity | Type | Description |
| d6s | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,14
uwall_s_agThe UPPER_WALLS action with label uwall_s_ag calculates the following quantities:| Quantity | Type | Description |
| uwall_s_ag.bias | scalar | the instantaneous value of the bias potential |
| uwall_s_ag.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
uwall_aThe UPPER_WALLS action with label uwall_a calculates the following quantities:| Quantity | Type | Description |
| uwall_a.bias | scalar | the instantaneous value of the bias potential |
| uwall_a.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
lwall_aThe LOWER_WALLS action with label lwall_a calculates the following quantities:| Quantity | Type | Description |
| lwall_a.bias | scalar | the instantaneous value of the bias potential |
| lwall_a.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
lwall_a2The LOWER_WALLS action with label lwall_a2 calculates the following quantities:| Quantity | Type | Description |
| lwall_a2.bias | scalar | the instantaneous value of the bias potential |
| lwall_a2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:| Quantity | Type | Description |
| lwall.bias | scalar | the instantaneous value of the bias potential |
| lwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Type | Description |
| uwall.bias | scalar | the instantaneous value of the bias potential |
| uwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
lwallcnThe LOWER_WALLS action with label lwallcn calculates the following quantities:| Quantity | Type | Description |
| lwallcn.bias | scalar | the instantaneous value of the bias potential |
| lwallcn.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
lwallcsThe LOWER_WALLS action with label lwallcs calculates the following quantities:| Quantity | Type | Description |
| lwallcs.bias | scalar | the instantaneous value of the bias potential |
| lwallcs.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
uwallnThe UPPER_WALLS action with label uwalln calculates the following quantities:| Quantity | Type | Description |
| uwalln.bias | scalar | the instantaneous value of the bias potential |
| uwalln.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
uwallsThe UPPER_WALLS action with label uwalls calculates the following quantities:| Quantity | Type | Description |
| uwalls.bias | scalar | the instantaneous value of the bias potential |
| uwalls.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
uwall_cnThe UPPER_WALLS action with label uwall_cn calculates the following quantities:| Quantity | Type | Description |
| uwall_cn.bias | scalar | the instantaneous value of the bias potential |
| uwall_cn.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
cn_wallThe LOWER_WALLS action with label cn_wall calculates the following quantities:| Quantity | Type | Description |
| cn_wall.bias | scalar | the instantaneous value of the bias potential |
| cn_wall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: 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
resThe RESTRAINT action with label res calculates the following quantities:| Quantity | Type | Description |
| res.bias | scalar | the instantaneous value of the bias potential |
| res.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. 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
res: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. 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 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
PRINTPrint 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=*
