Project ID: plumID:23.040
Source: plumed_metad/plumed_pyro.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001
The UNITS action with label calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-76 ENTITY1the atoms that make up a molecule that you wish to align=77-152 ENTITY2the atoms that make up a molecule that you wish to align=153-228 ENTITY3the atoms that make up a molecule that you wish to align=229-304 ENTITY4the atoms that make up a molecule that you wish to align=305-380 ENTITY5the atoms that make up a molecule that you wish to align=381-456
cal1The GROUP action with label cal1 calculates the following quantities:| Quantity | Type | Description |
| cal1 | 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=1-76
cal2The GROUP action with label cal2 calculates the following quantities:| Quantity | Type | Description |
| cal2 | 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=77-152
cal3The GROUP action with label cal3 calculates the following quantities:| Quantity | Type | Description |
| cal3 | 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=153-228
cal4The GROUP action with label cal4 calculates the following quantities:| Quantity | Type | Description |
| cal4 | 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=229-304
cal5The GROUP action with label cal5 calculates the following quantities:| Quantity | Type | Description |
| cal5 | 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=305-380
cal6The GROUP action with label cal6 calculates the following quantities:| Quantity | Type | Description |
| cal6 | 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=381-456
com1The COM action with label com1 calculates the following quantities:| Quantity | Type | Description |
| com1 | 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=cal1
com2The COM action with label com2 calculates the following quantities:| Quantity | Type | Description |
| com2 | 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=cal2
com3The COM action with label com3 calculates the following quantities:| Quantity | Type | Description |
| com3 | 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=cal3
com4The COM action with label com4 calculates the following quantities:| Quantity | Type | Description |
| com4 | 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=cal4
com5The COM action with label com5 calculates the following quantities:| Quantity | Type | Description |
| com5 | 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=cal5
com6The COM action with label com6 calculates the following quantities:| Quantity | Type | Description |
| com6 | 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=cal6
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=com1,com2
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=com1,com3
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=com1,com4
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=com1,com5
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=com1,com6
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=com2,com3
d7The DISTANCE action with label d7 calculates the following quantities:| Quantity | Type | Description |
| d7 | 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=com2,com4
d8The DISTANCE action with label d8 calculates the following quantities:| Quantity | Type | Description |
| d8 | 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=com2,com5
d9The DISTANCE action with label d9 calculates the following quantities:| Quantity | Type | Description |
| d9 | 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=com2,com6
d10The DISTANCE action with label d10 calculates the following quantities:| Quantity | Type | Description |
| d10 | 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=com3,com4
d11The DISTANCE action with label d11 calculates the following quantities:| Quantity | Type | Description |
| d11 | 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=com3,com5
d12The DISTANCE action with label d12 calculates the following quantities:| Quantity | Type | Description |
| d12 | 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=com3,com6
d13The DISTANCE action with label d13 calculates the following quantities:| Quantity | Type | Description |
| d13 | 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=com4,com5
d14The DISTANCE action with label d14 calculates the following quantities:| Quantity | Type | Description |
| d14 | 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=com4,com6
d15The DISTANCE action with label d15 calculates the following quantities:| Quantity | Type | Description |
| d15 | 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=com5,com6
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=mul_distThe DISTANCES action with label mul_dist calculates the following quantities:| Quantity | Type | Description |
| mul_dist | vector | the DISTANCES between the each pair of atoms that were specified |
| mul_dist_between-1 | scalar | the number of colvars that have a value that lies in a particular interval |
| mul_dist_between-2 | scalar | the number of colvars that have a value that lies in a particular interval |
ATOMS1the pairs of atoms that you would like to calculate the angles for=com1,com2
ATOMS2the pairs of atoms that you would like to calculate the angles for=com1,com3
ATOMS3the pairs of atoms that you would like to calculate the angles for=com1,com4
ATOMS4the pairs of atoms that you would like to calculate the angles for=com1,com5
ATOMS5the pairs of atoms that you would like to calculate the angles for=com1,com6
ATOMS6the pairs of atoms that you would like to calculate the angles for=com2,com3
ATOMS7the pairs of atoms that you would like to calculate the angles for=com2,com4
ATOMS8the pairs of atoms that you would like to calculate the angles for=com2,com5
ATOMS9the pairs of atoms that you would like to calculate the angles for=com2,com6
ATOMS10the pairs of atoms that you would like to calculate the angles for=com3,com4
ATOMS11the pairs of atoms that you would like to calculate the angles for=com3,com5
ATOMS12the pairs of atoms that you would like to calculate the angles for=com3,com6
ATOMS13the pairs of atoms that you would like to calculate the angles for=com4,com5
ATOMS14the pairs of atoms that you would like to calculate the angles for=com4,com6
ATOMS15the pairs of atoms that you would like to calculate the angles for=com5,com6
BETWEEN1calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=9. UPPER=12.5}
BETWEEN2calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.={GAUSSIAN LOWER=13. UPPER=17}
... DISTANCES
# DISTANCES ...
mul_dist_vatom1The CENTER_FAST action with label mul_dist_vatom1 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom1 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com1,com2
mul_dist_vatom2The CENTER_FAST action with label mul_dist_vatom2 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom2 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com1,com3
mul_dist_vatom3The CENTER_FAST action with label mul_dist_vatom3 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom3 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com1,com4
mul_dist_vatom4The CENTER_FAST action with label mul_dist_vatom4 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom4 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com1,com5
mul_dist_vatom5The CENTER_FAST action with label mul_dist_vatom5 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom5 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com1,com6
mul_dist_vatom6The CENTER_FAST action with label mul_dist_vatom6 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom6 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com2,com3
mul_dist_vatom7The CENTER_FAST action with label mul_dist_vatom7 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom7 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com2,com4
mul_dist_vatom8The CENTER_FAST action with label mul_dist_vatom8 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom8 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com2,com5
mul_dist_vatom9The CENTER_FAST action with label mul_dist_vatom9 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom9 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com2,com6
mul_dist_vatom10The CENTER_FAST action with label mul_dist_vatom10 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom10 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com3,com4
mul_dist_vatom11The CENTER_FAST action with label mul_dist_vatom11 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom11 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com3,com5
mul_dist_vatom12The CENTER_FAST action with label mul_dist_vatom12 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom12 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com3,com6
mul_dist_vatom13The CENTER_FAST action with label mul_dist_vatom13 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom13 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com4,com5
mul_dist_vatom14The CENTER_FAST action with label mul_dist_vatom14 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom14 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com4,com6
mul_dist_vatom15The CENTER_FAST action with label mul_dist_vatom15 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_vatom15 | atoms | virtual atom calculated by CENTER_FAST action |
: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=com5,com6
mul_dist_grpThe GROUP action with label mul_dist_grp calculates the following quantities:| Quantity | Type | Description |
| mul_dist_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=mul_dist_vatom1,mul_dist_vatom2,mul_dist_vatom3,mul_dist_vatom4,mul_dist_vatom5,mul_dist_vatom6,mul_dist_vatom7,mul_dist_vatom8,mul_dist_vatom9,mul_dist_vatom10,mul_dist_vatom11,mul_dist_vatom12,mul_dist_vatom13,mul_dist_vatom14,mul_dist_vatom15
mul_distThe DISTANCE action with label mul_dist calculates the following quantities:| Quantity | Type | Description |
| mul_dist | 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=com1,com2 ATOMS2the pair of atom that we are calculating the distance between=com1,com3 ATOMS3the pair of atom that we are calculating the distance between=com1,com4 ATOMS4the pair of atom that we are calculating the distance between=com1,com5 ATOMS5the pair of atom that we are calculating the distance between=com1,com6
mul_dist_bt1The BETWEEN action with label mul_dist_bt1 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_bt1 | vector | the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors |
: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=mul_dist SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=9. UPPER=12.5}
mul_dist_between-1The SUM action with label mul_dist_between-1 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_between-1 | 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=mul_dist_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
mul_dist_bt2The BETWEEN action with label mul_dist_bt2 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_bt2 | vector | the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors |
: BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=mul_dist SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=13. UPPER=17}
mul_dist_between-2The SUM action with label mul_dist_between-2 calculates the following quantities:| Quantity | Type | Description |
| mul_dist_between-2 | 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=mul_dist_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=mul_dist.between-1,mul_dist.between-2
GRID_MINthe lower bounds for the grid=0,0
GRID_MAXthe upper bounds for the grid=20,20,
SIGMAthe widths of the Gaussian hills=0.1,0.1
HEIGHTthe heights of the Gaussian hills=1.5
BIASFACTORuse well tempered metadynamics and use this bias factor=30
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.
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 |
| metad.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
| metad.rct | scalar | the reweighting factor c(t). |
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
PACEthe frequency for hill addition=500
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=mul_dist.between-1,mul_dist.between-2
GRID_MINthe lower bounds for the grid=0,0
GRID_MAXthe upper bounds for the grid=20,20,
SIGMAthe widths of the Gaussian hills=0.1,0.1
HEIGHTthe heights of the Gaussian hills=1.5
BIASFACTORuse well tempered metadynamics and use this bias factor=30
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.
LABELa label for the action so that its output can be referenced in the input to other actions=metad
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
PACEthe frequency for hill addition=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=mul_dist.between-1,mul_dist.between-2,metad.* FILEthe name of the file on which to output these quantities=metad_data.dat STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15 FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500
FLUSHThis 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=500
