Project ID: plumID:24.001
Source: chorismate_mutase/opes_flooding_qmmm/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A d1 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5663,5675 d2 : DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5670,5671 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=+3.60 KAPPAthe force constant for the wall=250.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_C-C5
dd : COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2 COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO chi_exc : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dd FUNCthe function you wish to evaluate=step(-x+0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO opesOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ... ARGthe labels of the scalars on which the bias will act=dd PACEthe frequency for kernel deposition=100 ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=200 BARRIERthe free energy barrier to be overcome=45 EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc TEMP temperature=300.0 STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=RESTART_INFO STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=100 ... :
COMMITTORDoes a committor analysis. More details ... ARGthe labels of the values which is being used to define the committor surface=dd STRIDE the frequency with which the CVs are analyzed=10 BASIN_LL1List of lower limits for basin #=-10.0 BASIN_UL1List of upper limits for basin #=-2.0 ... COMMITTOR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,dd,opes.*,uwall_C-C5.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1