PLUMED-NEST

Project ID: plumID:25.024
Source: A2G2S2_longbox.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

com1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-288
The COM action with label com1 calculates somethingcom2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=289-576
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The COM action with label com2 calculates somethingp1: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=com1 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.x
the x-component of the atom position
p1.y
the y-component of the atom position
p1.z
the z-component of the atom position
p1.a
the normalized projection on the first lattice vector of the atom position
p1.b
the normalized projection on the second lattice vector of the atom position
p1.c
the normalized projection on the third lattice vector of the atom positionp2: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=com2 SCALED_COMPONENTS calculate the a, b and c scaled components of the position separately and store them as label
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The POSITION action with label p2 calculates the following quantities:
 Quantity   
 Description  
p2.x
the x-component of the atom position
p2.y
the y-component of the atom position
p2.z
the z-component of the atom position
p2.a
the normalized projection on the first lattice vector of the atom position
p2.b
the normalized projection on the second lattice vector of the atom position
p2.c
the normalized projection on the third lattice vector of the atom positionrestraint: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=p1.a,p1.b,p2.a,p2.b ATthe position of the restraint=0.5,0.5,0.5,0.5 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=500,500,500,500
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The RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the bias potential
restraint.force2
the instantaneous value of the squared force due to this bias potentialdistance: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com1,com2
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The DISTANCE action with label distance calculates the following quantities:
 Quantity   
 Description  
distance.value
the DISTANCE between this pair of atomsds: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com1,com2 SCALED_COMPONENTS calculate the a, b and c scaled components of the distance separately and store them as label
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The DISTANCE action with label ds calculates the following quantities:
 Quantity   
 Description  
ds.a
the normalized projection on the first lattice vector of the vector connecting the two atoms
ds.b
the normalized projection on the second lattice vector of the vector connecting the two atoms
ds.c
the normalized projection on the third lattice vector of the vector connecting the two atoms
ds.value
the DISTANCE between this pair of atomsdsz: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ds.c PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-0.5,0.5
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The COMBINE action with label dsz calculates the following quantities:
 Quantity   
 Description  
dsz.value
a linear combinationbias: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=dsz TAUin well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau=4.0 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=1 GRID_MINthe lower bounds for the grid=-0.5 GRID_MAXthe upper bounds for the grid=0.5 GRID_BINthe number of bins for the grid=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 RECTlist of bias factors for all the replicas=1,1.29,1.67,2.16,2.78,3.60,4.65,6 FILE a file in which the list of added hills is stored=HILLS_distance CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
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The METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.bias
the instantaneous value of the bias potential
bias.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
bias.rct
the reweighting factor c(t)PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=distance,ds.*,dsz 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

The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=p1.a,p1.b,p1.c,p2.a,p2.b,p2.c,restraint.*,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=BIAS