**Project ID:** plumID:19.050

**Source:** plumed_metad.dat

**Originally used with PLUMED version:** not specified

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

# The two lines below instruct PLUMED to calculate the distance between # the adsorbate and the isosurface. Notice how, as discussed in the main text, # only a subset of the atoms in the membrane are used when we calculate the # density as this reduces the computational expense.d1:DENSITYCalculate functions of the density of atoms as a function of the box. This allows one to calculate More detailsSPECIES=2-2400:12,10-2400:12this keyword is used for colvars such as coordination numberLOWMEMlower the memory requirementscont:DISTANCE_FROM_CONTOUR...Calculate the perpendicular distance from a Willard-Chandler dividing surface. More detailsDATA=The input base multicolvar which is being used to calculate the contourd1ATOM=2413The atom whose perpendicular distance we are calculating from the contourBANDWIDTH=3.0,3.0,3.0the bandwidths for kernel density estimationDIR=zthe direction perpendicular to the contour that you are looking forCONTOUR=0.42 ... # This command instructs PLUMED to construct a metadynamics bias that is a # function of the CV that is used in the main text. In order to reduce the # computational expense this bias is stored on a grid. Furthermore, adaptive # hills are used to ensure faster convergence of the final free energy surfacethe value we would like for the contourmm: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 actionscont.qdistSIGMA=0.5the widths of the Gaussian hillsHEIGHT=1.3the heights of the Gaussian hillsPACE=100the frequency for hill additionBIASFACTOR=25use well tempered metadynamics and use this bias factorTEMP=325the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=-15.0the lower bounds for the gridGRID_MAX=100.0the upper bounds for the gridGRID_BIN=115000the number of bins for the gridADAPTIVE=GEOMuse a geometric (=GEOM) or diffusion (=DIFF) based hills width schemeSIGMA_MIN=0.05the lower bounds for the sigmas (in CV units) when using adaptive hillsSIGMA_MAX=6.00 ... # This command instructs PLUMED to add a restraint that prevents the collective # variable from taking high values. This restraint thus prevents the adsorbate # from moving too far from the membrane surface.the upper bounds for the sigmas (in CV units) when using adaptive hillsuwall:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the input for this action is the scalar output from one or more other actionscont.qdistAT=50.0the positions of the wallKAPPA=1.0the force constant for the wallEXP=2 # This command prints the value of the collective variable and the metadynamics # bias to a file called colvarthe powers for the wallsPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionscont.*,mmSTRIDE=20the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities