Project ID: plumID:23.035
Source: Y4R_SRS_Gi/MW-WT-MetaD_Y4R-SRS-Gi/plumed.dat
Originally used with PLUMED version: 2.7.3
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
#RESTART
WHOLEMOLECULESThis 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=1 ENTITY0the atoms that make up a molecule that you wish to align=1-10746

c1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=4088,1562 NOPBC ignore the periodic boundary conditions when calculating distances # center 252TRP-99VAL
d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,127 COMPONENTS calculate the x, y and z components of the distance separately and store them as label NOPBC ignore the periodic boundary conditions when calculating distances # c1 7TYR CA peptide

###FUNNEL_PARAMETERS### s_cent: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=6.5 # INFLEXION beta_cent: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=2.0 # STEEPNESS wall_width: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.5 # WIDTH (h) wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.15 # BUFFER (f, total width = WIDTH + BUFFER) lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 # Lower Wall (the starting point of the funnel) uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=11.5 KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 # Upper Wall (the ending point of the funnel)
###########CALCULATE FUNNEL####### MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=wall_center ARGthe values input to this function=d1.z,s_cent,beta_cent,wall_width,wall_buffer VARthe names to give each of the arguments in the function=s,sc,b,h,f FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
########BIAS OF THE WALL###### wall_height: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=100.0 wall_steepness: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUEthe single number that you would like to store=500.0
#######PROYECTION DXY########## MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=dxy ARGthe values input to this function=d1.x,d1.y VARthe names to give each of the arguments in the function=ax,ay FUNCthe function you wish to evaluate=(sqrt(ax*ax+ay*ay)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
#######DEFINE_POTENTIAL####### MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=wall_bias ARGthe values input to this function=dxy,wall_height,wall_steepness,wall_center VARthe names to give each of the arguments in the function=z,h,b,zc FUNCthe function you wish to evaluate=h*(1.-(1./(1.+exp(b*(z-zc))))) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ... MATHEVAL
finalbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias ########DEFINE_METAD########### METADUsed to performed metadynamics on one or more collective variables. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=meta ARGthe labels of the scalars on which the bias will act=d1.z SIGMAthe widths of the Gaussian hills=0.1 HEIGHTthe heights of the Gaussian hills=2 PACEthe frequency for hill addition=500 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=10.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 GRID_MINthe lower bounds for the grid=-1 GRID_MAXthe upper bounds for the grid=12 GRID_BINthe number of bins for the grid=300 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR ... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR