Project ID: plumID:21.045
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
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=5,10
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=5,15
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=10,15
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
ATthe positions of the wall=0.6,0.6,0.6
KAPPAthe force constant for the wall=100000.0,100000.0,100000.0
LABELa label for the action so that its output can be referenced in the input to other actions=uwall-distThe UPPER_WALLS action with label uwall-dist calculates the following quantities:| Quantity | Type | Description |
| uwall-dist.bias | scalar | the instantaneous value of the bias potential |
| uwall-dist.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... UPPER_WALLS
sum_distThe COMBINE action with label sum_dist calculates the following quantities:| Quantity | Type | Description |
| sum_dist | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=sum_dist
ATthe positions of the wall=0.9
KAPPAthe force constant for the wall=100000
LABELa label for the action so that its output can be referenced in the input to other actions=lwall-sum_distThe LOWER_WALLS action with label lwall-sum_dist calculates the following quantities:| Quantity | Type | Description |
| lwall-sum_dist.bias | scalar | the instantaneous value of the bias potential |
| lwall-sum_dist.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... LOWER_WALLS
c1The COORDINATION action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | 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)=10,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20
c1: 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)=10,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20 D_0 The d_0 parameter of the switching function=0.0
c2The COORDINATION action with label c2 calculates the following quantities:| Quantity | Type | Description |
| c2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20
c2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20 D_0 The d_0 parameter of the switching function=0.0
c3The COORDINATION action with label c3 calculates the following quantities:| Quantity | Type | Description |
| c3 | 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)=5,10 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20
c3: 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)=5,10 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20 D_0 The d_0 parameter of the switching function=0.0
coord-sumThe COMBINE action with label coord-sum calculates the following quantities:| Quantity | Type | Description |
| coord-sum | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=c1,c2,c3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=coord-sum ATthe positions of the wall=1.82 KAPPAthe force constant for the wall=20000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall-coordThe LOWER_WALLS action with label lwall-coord calculates the following quantities:| Quantity | Type | Description |
| lwall-coord.bias | scalar | the instantaneous value of the bias potential |
| lwall-coord.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=c1,c2,c3
ATthe positions of the wall=1.8,1.8,1.8
KAPPAthe force constant for the wall=50000,50000,50000
LABELa label for the action so that its output can be referenced in the input to other actions=uwall-coordThe UPPER_WALLS action with label uwall-coord calculates the following quantities:| Quantity | Type | Description |
| uwall-coord.bias | scalar | the instantaneous value of the bias potential |
| uwall-coord.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... UPPER_WALLS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,c1,c2,c3,coord-sum,lwall-coord.bias,uwall-coord.bias,uwall-dist.bias,lwall-sum_dist.bias STRIDE the frequency with which the quantities of interest should be output=20 FILEthe name of the file on which to output these quantities=coord_s-s.dat
The PRINT action with label calculates somethingcys1-coordThe COORDINATIONNUMBER action with label cys1-coord calculates the following quantities:| Quantity | Type | Description |
| cys1-coord | vector | the coordination numbers of the specified atoms |
| cys1-coord_mean | scalar | the mean 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=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1,3,4 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities
cys1-coord: 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=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1,3,4 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# cys1-coord: COORDINATIONNUMBER SPECIESA=2 SPECIESB=1,3,4 R_0=0.130 NN=45 MM=90 MEAN
cys1-coord_grpThe GROUP action with label cys1-coord_grp calculates the following quantities:| Quantity | Type | Description |
| cys1-coord_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=2
cys1-coord_matThe CONTACT_MATRIX action with label cys1-coord_mat calculates the following quantities:| Quantity | Type | Description |
| cys1-coord_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=2 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=1,3,4 R_0The r_0 parameter of the switching function=0.130 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90
cys1-coord_onesThe CONSTANT action with label cys1-coord_ones calculates the following quantities:| Quantity | Type | Description |
| cys1-coord_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=3
cys1-coordThe MATRIX_VECTOR_PRODUCT action with label cys1-coord calculates the following quantities:| Quantity | Type | Description |
| cys1-coord | 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=cys1-coord_mat,cys1-coord_ones
cys1-coord_caverageThe MEAN action with label cys1-coord_caverage calculates the following quantities:| Quantity | Type | Description |
| cys1-coord_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=cys1-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cys1-coord_meanThe MEAN action with label cys1-coord_mean calculates the following quantities:| Quantity | Type | Description |
| cys1-coord_mean | 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=cys1-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cys2-coordThe COORDINATIONNUMBER action with label cys2-coord calculates the following quantities:| Quantity | Type | Description |
| cys2-coord | vector | the coordination numbers of the specified atoms |
| cys2-coord_mean | scalar | the mean 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=7 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=6,8,9 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities
cys2-coord: 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=7 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=6,8,9 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# cys2-coord: COORDINATIONNUMBER SPECIESA=7 SPECIESB=6,8,9 R_0=0.130 NN=45 MM=90 MEAN
cys2-coord_grpThe GROUP action with label cys2-coord_grp calculates the following quantities:| Quantity | Type | Description |
| cys2-coord_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=7
cys2-coord_matThe CONTACT_MATRIX action with label cys2-coord_mat calculates the following quantities:| Quantity | Type | Description |
| cys2-coord_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=7 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=6,8,9 R_0The r_0 parameter of the switching function=0.130 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90
cys2-coord_onesThe CONSTANT action with label cys2-coord_ones calculates the following quantities:| Quantity | Type | Description |
| cys2-coord_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=3
cys2-coordThe MATRIX_VECTOR_PRODUCT action with label cys2-coord calculates the following quantities:| Quantity | Type | Description |
| cys2-coord | 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=cys2-coord_mat,cys2-coord_ones
cys2-coord_caverageThe MEAN action with label cys2-coord_caverage calculates the following quantities:| Quantity | Type | Description |
| cys2-coord_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=cys2-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cys2-coord_meanThe MEAN action with label cys2-coord_mean calculates the following quantities:| Quantity | Type | Description |
| cys2-coord_mean | 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=cys2-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cys3-coordThe COORDINATIONNUMBER action with label cys3-coord calculates the following quantities:| Quantity | Type | Description |
| cys3-coord | vector | the coordination numbers of the specified atoms |
| cys3-coord_mean | scalar | the mean 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=12 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=11,13,14 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities
cys3-coord: 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=12 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=11,13,14 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# cys3-coord: COORDINATIONNUMBER SPECIESA=12 SPECIESB=11,13,14 R_0=0.130 NN=45 MM=90 MEAN
cys3-coord_grpThe GROUP action with label cys3-coord_grp calculates the following quantities:| Quantity | Type | Description |
| cys3-coord_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=12
cys3-coord_matThe CONTACT_MATRIX action with label cys3-coord_mat calculates the following quantities:| Quantity | Type | Description |
| cys3-coord_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=12 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=11,13,14 R_0The r_0 parameter of the switching function=0.130 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90
cys3-coord_onesThe CONSTANT action with label cys3-coord_ones calculates the following quantities:| Quantity | Type | Description |
| cys3-coord_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=3
cys3-coordThe MATRIX_VECTOR_PRODUCT action with label cys3-coord calculates the following quantities:| Quantity | Type | Description |
| cys3-coord | 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=cys3-coord_mat,cys3-coord_ones
cys3-coord_caverageThe MEAN action with label cys3-coord_caverage calculates the following quantities:| Quantity | Type | Description |
| cys3-coord_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=cys3-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cys3-coord_meanThe MEAN action with label cys3-coord_mean calculates the following quantities:| Quantity | Type | Description |
| cys3-coord_mean | 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=cys3-coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=cys1-coord.mean,cys2-coord.mean,cys3-coord.mean
ATthe positions of the wall=2.5,2.5,2.5
KAPPAthe force constant for the wall=50000,50000,50000
LABELa label for the action so that its output can be referenced in the input to other actions=lwall-HBThe LOWER_WALLS action with label lwall-HB calculates the following quantities:| Quantity | Type | Description |
| lwall-HB.bias | scalar | the instantaneous value of the bias potential |
| lwall-HB.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... LOWER_WALLS
S1-2HB1The DISTANCE action with label S1-2HB1 calculates the following quantities:| Quantity | Type | Description |
| S1-2HB1 | 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=5,6
S1-2HB2The DISTANCE action with label S1-2HB2 calculates the following quantities:| Quantity | Type | Description |
| S1-2HB2 | 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=5,8
S1-2HB3The DISTANCE action with label S1-2HB3 calculates the following quantities:| Quantity | Type | Description |
| S1-2HB3 | 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=5,9
S1-3HB1The DISTANCE action with label S1-3HB1 calculates the following quantities:| Quantity | Type | Description |
| S1-3HB1 | 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=5,11
S1-3HB2The DISTANCE action with label S1-3HB2 calculates the following quantities:| Quantity | Type | Description |
| S1-3HB2 | 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=5,13
S1-3HB3The DISTANCE action with label S1-3HB3 calculates the following quantities:| Quantity | Type | Description |
| S1-3HB3 | 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=5,14
S2-1HB1The DISTANCE action with label S2-1HB1 calculates the following quantities:| Quantity | Type | Description |
| S2-1HB1 | 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=10,1
S2-1HB2The DISTANCE action with label S2-1HB2 calculates the following quantities:| Quantity | Type | Description |
| S2-1HB2 | 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=10,3
S2-1HB3The DISTANCE action with label S2-1HB3 calculates the following quantities:| Quantity | Type | Description |
| S2-1HB3 | 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=10,4
S2-3HB1The DISTANCE action with label S2-3HB1 calculates the following quantities:| Quantity | Type | Description |
| S2-3HB1 | 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=10,11
S2-3HB2The DISTANCE action with label S2-3HB2 calculates the following quantities:| Quantity | Type | Description |
| S2-3HB2 | 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=10,13
S2-3HB3The DISTANCE action with label S2-3HB3 calculates the following quantities:| Quantity | Type | Description |
| S2-3HB3 | 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=10,14
S3-2HB1The DISTANCE action with label S3-2HB1 calculates the following quantities:| Quantity | Type | Description |
| S3-2HB1 | 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=15,6
S3-2HB2The DISTANCE action with label S3-2HB2 calculates the following quantities:| Quantity | Type | Description |
| S3-2HB2 | 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=15,8
S3-2HB3The DISTANCE action with label S3-2HB3 calculates the following quantities:| Quantity | Type | Description |
| S3-2HB3 | 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=15,9
S3-1HB1The DISTANCE action with label S3-1HB1 calculates the following quantities:| Quantity | Type | Description |
| S3-1HB1 | 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=15,1
S3-1HB2The DISTANCE action with label S3-1HB2 calculates the following quantities:| Quantity | Type | Description |
| S3-1HB2 | 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=15,3
S3-1HB3The DISTANCE action with label S3-1HB3 calculates the following quantities:| Quantity | Type | Description |
| S3-1HB3 | 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=15,4
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=S1-2HB1,S1-2HB2,S1-2HB3,S1-3HB1,S1-3HB2,S1-3HB3,S2-1HB1,S2-1HB2,S2-1HB3,S2-3HB1,S2-3HB2,S2-3HB3,S3-2HB1,S3-2HB2,S3-2HB3,S3-1HB1,S3-1HB2,S3-1HB3
ATthe positions of the wall=0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3
KAPPAthe force constant for the wall=50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000
LABELa label for the action so that its output can be referenced in the input to other actions=lwall_S-HBThe LOWER_WALLS action with label lwall_S-HB calculates the following quantities:| Quantity | Type | Description |
| lwall_S-HB.bias | scalar | the instantaneous value of the bias potential |
| lwall_S-HB.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... LOWER_WALLS
S1-CB2The DISTANCE action with label S1-CB2 calculates the following quantities:| Quantity | Type | Description |
| S1-CB2 | 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=5,7
S1-CB3The DISTANCE action with label S1-CB3 calculates the following quantities:| Quantity | Type | Description |
| S1-CB3 | 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=5,12
S2-CB1The DISTANCE action with label S2-CB1 calculates the following quantities:| Quantity | Type | Description |
| S2-CB1 | 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=10,2
S2-CB3The DISTANCE action with label S2-CB3 calculates the following quantities:| Quantity | Type | Description |
| S2-CB3 | 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=10,12
S3-CB1The DISTANCE action with label S3-CB1 calculates the following quantities:| Quantity | Type | Description |
| S3-CB1 | 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=15,2
S3-CB2The DISTANCE action with label S3-CB2 calculates the following quantities:| Quantity | Type | Description |
| S3-CB2 | 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=15,7
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2
ATthe positions of the wall=0.3,0.3,0.3,0.3,0.3,0.3
KAPPAthe force constant for the wall=50000,50000,50000,50000,50000,50000
LABELa label for the action so that its output can be referenced in the input to other actions=lwall_S-CBThe LOWER_WALLS action with label lwall_S-CB calculates the following quantities:| Quantity | Type | Description |
| lwall_S-CB.bias | scalar | the instantaneous value of the bias potential |
| lwall_S-CB.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... LOWER_WALLS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2,lwall_S-CB.bias,lwall_S-HB.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=cb-s_hb-s_dist.dat
nd1The DISTANCE action with label nd1 calculates the following quantities:| Quantity | Type | Description |
| nd1 | 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=5,2650
nd2The DISTANCE action with label nd2 calculates the following quantities:| Quantity | Type | Description |
| nd2 | 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=10,2650
nd3The DISTANCE action with label nd3 calculates the following quantities:| Quantity | Type | Description |
| nd3 | 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=15,2650
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ...
ARGthe arguments on which the bias is acting=nd1,nd2,nd3
ATthe positions of the wall=1.2,1.2,1.2
KAPPAthe force constant for the wall=100000.0,100000.0,100000.0
LABELa label for the action so that its output can be referenced in the input to other actions=lwall-ndistThe LOWER_WALLS action with label lwall-ndist calculates the following quantities:| Quantity | Type | Description |
| lwall-ndist.bias | scalar | the instantaneous value of the bias potential |
| lwall-ndist.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
... LOWER_WALLS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nd1,nd2,nd3,lwall-ndist.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=ndist.dat
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
ARGthe labels of the scalars on which the bias will act=d1,d2,d3
HEIGHTthe heights of the Gaussian hills=0.5
SIGMAthe widths of the Gaussian hills=0.02,0.02,0.02
GRID_MINthe lower bounds for the grid=0.15,0.15,0.15
GRID_MAXthe upper bounds for the grid=0.7,0.7,0.7
GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.005,0.005
PACEthe frequency for hill addition=250
BIASFACTORuse well tempered metadynamics and use this bias factor=20
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
WALKERS_Nnumber of walkers=24
WALKERS_IDwalker id=0
WALKERS_DIRshared directory with the hills files from all the walkers=../
WALKERS_RSTRIDEstride for reading hills files=500
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad
ARGthe labels of the scalars on which the bias will act=d1,d2,d3
HEIGHTthe heights of the Gaussian hills=0.5
SIGMAthe widths of the Gaussian hills=0.02,0.02,0.02
GRID_MINthe lower bounds for the grid=0.15,0.15,0.15
GRID_MAXthe upper bounds for the grid=0.7,0.7,0.7
GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.005,0.005
PACEthe frequency for hill addition=250
BIASFACTORuse well tempered metadynamics and use this bias factor=20
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
WALKERS_Nnumber of walkers=24
WALKERS_IDwalker id=0
WALKERS_DIRshared directory with the hills files from all the walkers=../
WALKERS_RSTRIDEstride for reading hills files=500
FILE a file in which the list of added hills is stored=HILLS
... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,metad.bias,cys1-coord.mean,cys2-coord.mean,cys3-coord.mean,lwall-HB.bias 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
