Project ID: plumID:19.073
Source: Paper2_setup/plumed_aa.dat
Originally used with PLUMED version: 2.4
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.
DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCES action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCES between the each pair of atoms that were specified |
| d1_lowest | scalar | the smallest of the colvars |
GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-3,61-63 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=82,98,114,22,38,54 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
# DISTANCES LABEL=d1 GROUPA=1-3,61-63 GROUPB=82,98,114,22,38,54 LOWEST LOWMEM
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,82 ATOMS2the pair of atom that we are calculating the distance between=1,98 ATOMS3the pair of atom that we are calculating the distance between=1,114 ATOMS4the pair of atom that we are calculating the distance between=1,22 ATOMS5the pair of atom that we are calculating the distance between=1,38
d1_lowestThe LOWEST action with label d1_lowest calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1
# --- End of included input --- DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCES action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | vector | the DISTANCES between the each pair of atoms that were specified |
| d2_lowest | scalar | the smallest of the colvars |
GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-3 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=61-63 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
# DISTANCES LABEL=d2 GROUPA=1-3 GROUPB=61-63 LOWEST LOWMEM
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=1,61 ATOMS2the pair of atom that we are calculating the distance between=1,62 ATOMS3the pair of atom that we are calculating the distance between=1,63 ATOMS4the pair of atom that we are calculating the distance between=2,61 ATOMS5the pair of atom that we are calculating the distance between=2,62
d2_lowestThe LOWEST action with label d2_lowest calculates the following quantities:| Quantity | Type | Description |
| d2_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=d2
# --- End of included input --- 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 LABELa label for the action so that its output can be referenced in the input to other actions=cv1The COORDINATIONNUMBER action with label cv1 calculates the following quantities:| Quantity | Type | Description |
| cv1 | vector | the coordination numbers of the specified atoms |
| cv1_morethan | scalar | the number of colvars that have a value more than a threshold |
SPECIESAthe list of atoms for which the symmetry function is being calculated=1-3,61-63 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
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 LABELa label for the action so that its output can be referenced in the input to other actions=cv1 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-3,61-63 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0} 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
# COORDINATIONNUMBER LABEL=cv1 SPECIESA=1-3,61-63 SPECIESB=23,24,39,40,55,56,83,84,99,100,115,116 R_0=0.25 MORE_THAN={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
cv1_grpThe GROUP action with label cv1_grp calculates the following quantities:| Quantity | Type | Description |
| cv1_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=1-3,61-63
cv1_matThe CONTACT_MATRIX action with label cv1_mat calculates the following quantities:| Quantity | Type | Description |
| cv1_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=1-3,61-63 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=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 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
cv1_onesThe CONSTANT action with label cv1_ones calculates the following quantities:| Quantity | Type | Description |
| cv1_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=12
cv1The MATRIX_VECTOR_PRODUCT action with label cv1 calculates the following quantities:| Quantity | Type | Description |
| cv1 | 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=cv1_mat,cv1_ones
cv1_caverageThe MEAN action with label cv1_caverage calculates the following quantities:| Quantity | Type | Description |
| cv1_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=cv1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cv1_mtThe MORE_THAN action with label cv1_mt calculates the following quantities:| Quantity | Type | Description |
| cv1_mt | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cv1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
cv1_morethanThe SUM action with label cv1_morethan calculates the following quantities:| Quantity | Type | Description |
| cv1_morethan | 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=cv1_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=0.35 KAPPAthe force constant for the wall=150 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=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 |
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=150 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=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 |
METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=cv1.morethan,ene SIGMAthe widths of the Gaussian hills=0.01,200 HEIGHTthe heights of the Gaussian hills=2.5 PACEthe frequency for hill addition=500
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 |
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 BIASFACTORuse well tempered metadynamics and use this bias factor=100 FILE a file in which the list of added hills is stored=hills_aa
GRID_MINthe lower bounds for the grid=-0.5,-200000 GRID_MAXthe upper bounds for the grid=6,-120000 GRID_BINthe number of bins for the grid=526,350 GRID_SPARSE use a sparse grid to store hills
... METAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar_aa.dat
The PRINT action with label calculates somethingENDPLUMEDTerminate plumed input. More details
