Project ID: plumID:19.014
Source: mil-101_paper_setup/plumed_files/plumed_distances.dat
Originally used with PLUMED version: 2.2
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
RESTARTActivate restart. More details
The RESTART action with label calculates somethingDISTANCESCalculate 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 ---
METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=d1.lowest,d2.lowest SIGMAthe widths of the Gaussian hills=0.01,0.01 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=30 FILE a file in which the list of added hills is stored=hills
GRID_MINthe lower bounds for the grid=-0.1,-0.1 GRID_MAXthe upper bounds for the grid=6.0,6.0
GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.005 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=d1.lowest,d2.lowest,metad.bias FILEthe name of the file on which to output these quantities=colvar
ENDPLUMEDTerminate plumed input. More details
