Project ID: plumID:24.026
Source: CpHMD_metaD/scripts/PLUMED_GRID.dat
Originally used with PLUMED version: 2.9
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
tested onv2.10
tested onmaster
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# Check if the timesteps and temperature values are consistent with previous settings
# Activate MOLINFO functionalities
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=rep1.pdb
RESTARTActivate restart. More details # Do not remove this line. This is ignored for the first cycle in each block
chi:  TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8,9,19,28
puck: PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=6,8,9,13,11
# Activate well-tempered metadynamics in phi
metad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=chi,puck.Zx PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=2.0 SIGMAthe widths of the Gaussian hills=0.35,0.35 BIASFACTORuse well tempered metadynamics and use this bias factor=4 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=-pi,-pi GRID_MAXthe upper bounds for the grid=pi,pi GRID_WSTRIDEwrite the grid to a file every N steps=500 GRID_WFILEthe file on which to write the grid=GRID GRID_RFILEa grid file from which the bias should be read at the initial step of the simulation=GRID
   # Deposit a Gaussian every 500 time steps, with initial height 
   # equal to 1.2 kJ/mol and bias factor equal to 10 
   
   # Gaussian width (sigma) should be chosen based on the CV fluctuations in unbiased run 
   # try 1/2 or 1/3 of the estimated fluctuations 
   
   # Gaussians will be written to file and also stored on grid 

# Print both collective variables on COLVAR file every colvar_stride steps (Xps)
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=chi,puck.Zx,metad.bias  STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR