PLUMED-NEST

Project ID: plumID:21.001
Source: HS6ST/plumed.dat
Originally used with PLUMED version: 2.4
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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=refe_sel.pdb

The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=10 ENTITY0the atoms that make up a molecule that you wish to align=506,513,520,534,548,568,575,599,616,635,651,675,689,1737,1751,1771,1792,1813,1832,1846,1863,1882,1926,1932,1948,1959,1983,2004,2023,2034,2049,2073,2095,2112,2128,2145,3595,3615,3632,3656

# Assign atoms to group names.
# Chooses only the the water oxygens for coordination number with water (CN_W)
OW: 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=5523-27022:3
The GROUP action with label OW calculates somethingS: 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=5482 #paps sulfate
The GROUP action with label S calculates somethingG: 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=5460 #GlcNAc-acceptor oxygen
The GROUP action with label G calculates somethingT: 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=1248 #soluble exposed nitrogen from TRP
The GROUP action with label T calculates somethingene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingdP:   DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=S,G
The DISTANCE action with label dP calculates the following quantities:
 Quantity   
 Description  
dP.value
the DISTANCE between this pair of atomscn: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=T GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=0.261 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.6 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100

The COORDINATION action with label cn calculates the following quantities:
 Quantity   
 Description  
cn.value
the value of the coordinationRANDOM_EXCHANGESSet random pattern for exchanges. More details 
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=cvs.dat
metadP: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=dP,cn SIGMAthe widths of the Gaussian hills=0.1,0.1 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.5 BIASFACTORuse well tempered metadynamics and use this bias factor=5 GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=10,20 GRID_BINthe number of bins for the grid=100,100 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=50 FILE a file in which the list of added hills is stored=HILLS_dP3

The METAD action with label metadP calculates the following quantities:
 Quantity   
 Description  
metadP.bias
the instantaneous value of the bias potential
metadP.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metadP.rct
the reweighting factor c(t)LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dP ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=35100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dP ATthe positions of the wall=1.5 KAPPAthe force constant for the wall=35100 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=uwall.bias,lwall.bias FILEthe name of the file on which to output these quantities=bias STRIDE the frequency with which the quantities of interest should be output=100 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dP,cn STRIDE the frequency with which the quantities of interest should be output=100  FILEthe name of the file on which to output these quantities=COLVAR

bias: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=300
The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=dP
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=10
  GRID_BINthe number of bins for the grid=100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  LABELa label for the action so that its output can be referenced in the input to other actions=hB
... HISTOGRAM
The HISTOGRAM action with label hB calculates the following quantities:
 Quantity   
 Description  
hB.value
the estimate of the histogram as a function of the argument that was obtainedDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=hB FILE the file on which to write the grid=histoB STRIDE the frequency with which the grid should be output to the file=100 FMTthe format that should be used to output real numbers=%8.4f