**Project ID:** plumID:21.048

**Source:** plumed8.dat

**Originally used with PLUMED version:** 2.5

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

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

# plumed input for metadynamics amber prod run

# restart simulation (switch on after the first run to continue runs -reading from and appending to existing COLVAR and HILLS files) #RESTART

# change distance/position units of I/O to Angstroms (default nm)UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengths

# define virtual atom for centre of mass of lidocaine (=39atoms incl. H)lqz:COMCalculate the center of mass for a group of atoms. More detailsATOMS=18531-18569the list of atoms which are involved the virtual atom's definition

# define COM for point at base of vertical pore axis using CAatoms of 4x2x3 residues at bottom of each s5/6ax_base:COMCalculate the center of mass for a group of atoms. More detailsATOMS=2222,2239,2258,4418,4437,4456,7107,7121,7140,8594,8613,8633,11313,11332,11351,13359,13378,13398,16676,16683,16702,18275,18292,18313the list of atoms which are involved the virtual atom's definition

# define COM for point at top of vertical pore axis using CA of 4x6 residues on each P1ax_top:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947,12427,12434,12455,12474,12485,12504,17299,17310,17329,17348,17359,17378the list of atoms which are involved the virtual atom's definition

# define COM for point to define the transverse axis using CA of 2x6 residues on P1 of DI/DIIax_side:COMCalculate the center of mass for a group of atoms. More detailsATOMS=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947the list of atoms which are involved the virtual atom's definition

# Calculate distances of vectors between comsd_ax:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenax_top,ax_basedtop_lqz:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenax_top,lqzdbase_lqz:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenax_base,lqz

# Calculate position based on the projection along the vertical pore axisz:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input for this action is the scalar output from one or more other actionsdtop_lqz,dbase_lqz,d_axFUNC=(0.5*(y^2-x^2)/zthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function

# Calculate perpendicular distance of lqz from the vertical pore axisr:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG=the input for this action is the scalar output from one or more other actionsdtop_lqz,d_ax,zVAR=x,the names to give each of the arguments in the functionz,oFUNC=(sqrt(x^2-(z/2-o)^2the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function

# Calculate third positional parameter using torsional angletheta:TORSIONCalculate a torsional angle. More detailsAXIS=two atoms that define an axisax_top,ax_baseVECTOR1=two atoms that define a vectorax_top,ax_sideVECTOR2=two atoms that define a vectorax_base,lqz

# Add bias restraints to lqz position along s and z so it does not leave the pore interiorruwall: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 actionsrAT=18.0the positions of the wallKAPPA=100the force constant for the wallEXP=2the powers for the wallsrlwall:LOWER_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 actionsrAT=0.0the positions of the wallKAPPA=100the force constant for the wallEXP=2 # Should not be necessary; but might help prevent GPU errors ?the powers for the wallszlwall:LOWER_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 actionszAT=-12.0the positions of the wallKAPPA=100the force constant for the wallEXP=2the powers for the wallszuwall: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 actionszAT=12.0the positions of the wallKAPPA=100the force constant for the wallEXP=2the powers for the walls

# activate metadynamics 3D gaussian using 3 colvars:metad:METADUsed 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 actionsz,r,theta...PACE=500the frequency for hill additionHEIGHT=1.0 # Deposit a Gaussian every 500 time steps (eq to 2ps), with initial height equal to 1.0kJoule/molthe heights of the Gaussian hillsBIASFACTOR=15.0 # Bias factor used for well-tempered MetaD ## Lower the biasf the greater hillheights reduction - use higher value for faster sampling; lower value for better convergenceuse well tempered metadynamics and use this bias factorSIGMA=0.5,0.5,0.1 # Specify gaussian widths for each colvar (based on fluctuations during unbiased runs)the widths of the Gaussian hillsFILE=HILLS # Gaussians will be written to filea file in which the list of added hills is storedGRID_MIN=-18,-1.9,-pithe lower bounds for the gridGRID_MAX=18,24,pithe upper bounds for the gridGRID_SPACING=0.2,0.2,0.04 # Gaussians will be stored on grid with respective min/max/binsizes for each colvarthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)TEMP=310 # Temperature of system (required for well-tempered MetaD)the system temperature - this is only needed if you are doing well-tempered metadynamicsWALKERS_N=9number of walkersWALKERS_ID=8walker idWALKERS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=250 # Switch on Multiple Walkers MetaD with a total of 9 possible walkers, starting from walker#0; HILLS files read every 50steps=.2ps, written to DIR WHERE JOB WAS SUBMITTED # CALC_RCT RCT_USTRIDE=250 # Compute the reweighting factor and rbias every 250 timesteps using for histogram analysis --requires hills to be stored on GRID ...stride for reading hills files

# Print values of the colvars and all bias potentials on separate COLVAR files for each walkerPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsz,r,theta,*.biasFILE=COLVAR.8the name of the file on which to output these quantitiesSTRIDE=250the frequency with which the quantities of interest should be output