**Project ID:** plumID:23.039

**Source:** methane/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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=nvt.pdb # bias the distance of the 'methane molecule' from the center of the box #c1: CENTER ATOMS=5968a file in pdb format containing a reference structurec2:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=12204the group of atoms that you are calculating the Gyration Tensor fora1:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=1.75,1.65,1.50coordinates of the virtual atomd1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweena1,c2COMPONENTScalculate the x, y and z components of the distance separately and store them as labeltmp:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond1.x,d1.yPOWERS=2,2the powers to which you are raising each of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionrho:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiontmpPOWERS=0.5the powers to which you are raising each of the arguments in your functionPERIODIC=NO # since I don't see a spring constant defined in the SI of the paper, # I will use a spring constant of 2 kTif the output of your function is periodic then you should specify the periodicity of the functionuwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1.zAT=1.1the positions of the wallKAPPA=5000.0the force constant for the wallEXP=4the powers for the wallsp:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=the arguments on which the bias is actingrhoAT=0.0the position of the restraintKAPPA=418.4specifies that the restraint is harmonic and what the values of the force constants on each of the variables aremetad:METAD...Used to performed metadynamics on one or more collective variables. More detailsARG=the input for this action is the scalar output from one or more other actionsd1.z# Deposit a Gaussian every 300 time steps, with initial height equal to 2.0 kJ/molPACE=300the frequency for hill additionHEIGHT=2.0 # the bias factor should be chosen wiselythe heights of the Gaussian hillsBIASFACTOR=15use well tempered metadynamics and use this bias factorTEMP=300.0 # Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased runthe system temperature - this is only needed if you are doing well-tempered metadynamicsSIGMA=0.03 #Gaussians will be written to file and also stored on gridthe widths of the Gaussian hillsGRID_MIN=-1the lower bounds for the gridGRID_MAX=2.5the upper bounds for the gridCALC_RCT...calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]DUMPMASSCHARGEDump masses and charges on a selected file. More detailsFILE=mcfile # Print both collective variables and the value of the bias potential on COLVAR filefile on which to output charges and massesPrint quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=100the frequency with which the quantities of interest should be output