PLUMED-NEST-TEST-SITE

Project ID: plumID:25.009
Source: T1_MetaD/walker-1/plumed.dat
Originally used with PLUMED version: 2.8
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 somethinghThe GROUP action with label h calculates the following quantities:
 Quantity   
 Type   
 Description  
h
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=1,2,5,6,7,9,11,13,15,16,18,19,21,23,25,26,27,29,30,31,33,34,35,36,39,40,43,45,46,47,48,51,52,54,55,57,58,59,61,62,63,65,66,67,68,71,72,73,75,76,78,79,80,81,82,84,85,89,90,91,92,95,96,98,99,100,102,105,106,107,109,110,112,113,115,116,117,119,120,121,122,123,124,126,129,130,132,134,135,136,137,138,140,142,143,144,147,149,151,152,153,155,156,157,158,159,160,161,162,166,167,170,171,173,175,176,177,179,181,182,183,184,186,187,188,189
cv1The DISTANCE action with label cv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv1
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=192,193
cnThe COORDINATION action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=190,191 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=0.255 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=16
cn: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=190,191 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=0.255 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=16  D_0 The d_0 parameter of the switching function=0.0
cv2The CUSTOM action with label cv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv2
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cn FUNCthe function you wish to evaluate=x*0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no1The DISTANCE action with label no1 calculates the following quantities:
 Quantity   
 Type   
 Description  
no1
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=192,190
no2The DISTANCE action with label no2 calculates the following quantities:
 Quantity   
 Type   
 Description  
no2
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=192,191
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: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv1 ATthe positions of the wall=0.40 KAPPAthe force constant for the wall=10000.0
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall1.bias
scalar
the instantaneous value of the bias potential
uwall1.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=no1 ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=10000.0
uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall2.bias
scalar
the instantaneous value of the bias potential
uwall2.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=no2 ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=10000.0

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).: 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=cv1,cv2 SIGMAthe widths of the Gaussian hills=0.01,0.15 HEIGHTthe heights of the Gaussian hills=5.0 PACEthe frequency for hill addition=50 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 BIASFACTORuse well tempered metadynamics and use this bias factor=25 GRID_MINthe lower bounds for the grid=0.00,0.00 GRID_MAXthe upper bounds for the grid=0.5,7.0 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=10 WALKERS_Nnumber of walkers=2 WALKERS_IDwalker id=1 WALKERS_DIRshared directory with the hills files from all the walkers=../hills/ WALKERS_RSTRIDEstride for reading hills files=1000
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=cv1,cv2 SIGMAthe widths of the Gaussian hills=0.01,0.15 HEIGHTthe heights of the Gaussian hills=5.0 PACEthe frequency for hill addition=50 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 BIASFACTORuse well tempered metadynamics and use this bias factor=25 GRID_MINthe lower bounds for the grid=0.00,0.00 GRID_MAXthe upper bounds for the grid=0.5,7.0 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=10 WALKERS_Nnumber of walkers=2 WALKERS_IDwalker id=1 WALKERS_DIRshared directory with the hills files from all the walkers=../hills/ WALKERS_RSTRIDEstride for reading hills files=1000  FILE a file in which the list of added hills is stored=HILLS

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv1,cv2,metad.bias,metad.rbias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR_WALKER_1
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=50