PLUMED-NEST

Project ID: plumID:25.028
Source: C60/plumed_rg.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

# Define radius of gyration (Rg)
WHOLEMOLECULESThis 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=1-182
The WHOLEMOLECULES action with label  calculates somethingc1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=1-182

The CENTER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the position of the center of massWATER_OXYGENS: 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=183-68189:3

The GROUP action with label WATER_OXYGENS calculates somethingCOORD: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WATER_OXYGENS SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.60 NN=6 MM=12}

The COORDINATION action with label COORD calculates the following quantities:
 Quantity   
 Description  
COORD.value
the value of the coordinationrg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-182

#compute distance between CA atoms of residues 1 and 40
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsd: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,179
# Define end-to-end distance (d)
#d: DISTANCE ATOMS=1,40

#MOL: GROUP ATOMS=1-40

#WATER_OXYGENS: GROUP ATOMS=123-34511:3

#COORD: COORDINATION GROUPA=MOL GROUPB=WATER_OXYGENS R_0=0.6 


# Perform TICA on-the-fly using Rg, end-to-end distance, and num waters as input
#tica: TICA ARG=rg,d,num_waters NLAGS=10 DIM=2 STRIDE=10000

# Metadynamics bias potential along the first TICA component
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
the DISTANCE between this pair of atomsmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=rg SIGMAthe widths of the Gaussian hills=0.07 HEIGHTthe heights of the Gaussian hills=1.3 PACEthe frequency for hill addition=500 BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 GRID_MINthe lower bounds for the grid=0.2 GRID_MAXthe upper bounds for the grid=2.6 

# Print out collective variables for monitoring
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rg,COORD,d,metad.bias FILEthe name of the file on which to output these quantities=colvar2.dat STRIDE the frequency with which the quantities of interest should be output=1000