Project ID: plumID:22.037
Source: metad_setup/11bp_abasic-4_plumed.dat
Originally used with PLUMED version: 2.7
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
p1The DISTANCE action with label p1 calculates the following quantities:| Quantity | Type | Description |
| p1 | 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=2,63
p2The DISTANCE action with label p2 calculates the following quantities:| Quantity | Type | Description |
| p2 | 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=5,60
p3The DISTANCE action with label p3 calculates the following quantities:| Quantity | Type | Description |
| p3 | 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=8,57
p5The DISTANCE action with label p5 calculates the following quantities:| Quantity | Type | Description |
| p5 | 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=13,51
p6The DISTANCE action with label p6 calculates the following quantities:| Quantity | Type | Description |
| p6 | 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=16,48
p7The DISTANCE action with label p7 calculates the following quantities:| Quantity | Type | Description |
| p7 | 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=19,45
p8The DISTANCE action with label p8 calculates the following quantities:| Quantity | Type | Description |
| p8 | 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=22,42
p9The DISTANCE action with label p9 calculates the following quantities:| Quantity | Type | Description |
| p9 | 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=25,39
p10The DISTANCE action with label p10 calculates the following quantities:| Quantity | Type | Description |
| p10 | 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=28,36
p11The DISTANCE action with label p11 calculates the following quantities:| Quantity | Type | Description |
| p11 | 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=31,33
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_mean | scalar | the mean of the colvars |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ATOMS1the pairs of atoms that you would like to calculate the angles for=2,63 ATOMS2the pairs of atoms that you would like to calculate the angles for=5,60 ATOMS3the pairs of atoms that you would like to calculate the angles for=8,57 ATOMS4the pairs of atoms that you would like to calculate the angles for=13,51 ATOMS5the pairs of atoms that you would like to calculate the angles for=16,48 ATOMS6the pairs of atoms that you would like to calculate the angles for=19,45 ATOMS7the pairs of atoms that you would like to calculate the angles for=22,42 ATOMS8the pairs of atoms that you would like to calculate the angles for=25,39 ATOMS9the pairs of atoms that you would like to calculate the angles for=28,36 ATOMS10the pairs of atoms that you would like to calculate the angles for=31,33 MEAN calculate the mean of all the quantities
# d1: DISTANCES ATOMS1=2,63 ATOMS2=5,60 ATOMS3=8,57 ATOMS4=13,51 ATOMS5=16,48 ATOMS6=19,45 ATOMS7=22,42 ATOMS8=25,39 ATOMS9=28,36 ATOMS10=31,33 MEAN
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:| Quantity | Type | Description |
| d1_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=2,63
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:| Quantity | Type | Description |
| d1_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=5,60
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:| Quantity | Type | Description |
| d1_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=8,57
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:| Quantity | Type | Description |
| d1_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=13,51
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:| Quantity | Type | Description |
| d1_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=16,48
d1_vatom6The CENTER_FAST action with label d1_vatom6 calculates the following quantities:| Quantity | Type | Description |
| d1_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=19,45
d1_vatom7The CENTER_FAST action with label d1_vatom7 calculates the following quantities:| Quantity | Type | Description |
| d1_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=22,42
d1_vatom8The CENTER_FAST action with label d1_vatom8 calculates the following quantities:| Quantity | Type | Description |
| d1_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=25,39
d1_vatom9The CENTER_FAST action with label d1_vatom9 calculates the following quantities:| Quantity | Type | Description |
| d1_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=28,36
d1_vatom10The CENTER_FAST action with label d1_vatom10 calculates the following quantities:| Quantity | Type | Description |
| d1_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=31,33
d1_grpThe GROUP action with label d1_grp calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5,d1_vatom6,d1_vatom7,d1_vatom8,d1_vatom9,d1_vatom10
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=2,63 ATOMS2the pair of atom that we are calculating the distance between=5,60 ATOMS3the pair of atom that we are calculating the distance between=8,57 ATOMS4the pair of atom that we are calculating the distance between=13,51 ATOMS5the pair of atom that we are calculating the distance between=16,48
d1_meanThe MEAN action with label d1_mean calculates the following quantities:| Quantity | Type | Description |
| d1_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=d1 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. 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.mean
PACEthe frequency for hill addition=1000
HEIGHTthe heights of the Gaussian hills=0.5
SIGMAthe widths of the Gaussian hills=0.08
FILE a file in which the list of added hills is stored=HILLS
BIASFACTORuse well tempered metadynamics and use this bias factor=6.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=315.0
GRID_MINthe lower bounds for the grid=0.45
GRID_MAXthe upper bounds for the grid=7.5
... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1,p2,p3,p5,p6,p7,p8,p9,p10,p11,d1.mean,metad.bias STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR
