**Project ID:** plumID:21.045

**Source:** plumed.dat

**Originally used with PLUMED version:** 2.5.1

**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.

######################### ### S-S DISTANCES ### ### and WALLS ### #########################

### CYS1-CYS2 ###d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,10 ### CYS1-CYS3 ###the pair of atom that we are calculating the distance betweend2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,15 ### CYS2-CYS3 ###the pair of atom that we are calculating the distance betweend3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,15the pair of atom that we are calculating the distance between

# Upper Walls distancesUPPER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingd1,d2,d3AT=0.6,0.6,0.6the positions of the wallKAPPA=100000.0,100000.0,100000.0the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall-dist... UPPER_WALLSsum_dist:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functiond1,d2,d3PERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLOWER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingsum_distAT=0.9the positions of the wallKAPPA=100000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall-sum_dist... LOWER_WALLS

######################### ### S-S COORDINATION ### ### and WALLS ### #########################

### S1 Coord ###c1:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=5First list of atomsGROUPB=10,15Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.290The r_0 parameter of the switching functionNN=10The n parameter of the switching functionMM=20 ### S2 Coord ###The m parameter of the switching function; 0 implies 2*NNc2:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=10First list of atomsGROUPB=5,15Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.290The r_0 parameter of the switching functionNN=10The n parameter of the switching functionMM=20 ### S3 Coord ###The m parameter of the switching function; 0 implies 2*NNc3:COORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=15First list of atomsGROUPB=5,10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.290The r_0 parameter of the switching functionNN=10The n parameter of the switching functionMM=20The m parameter of the switching function; 0 implies 2*NN

### Sum of the three coordination nr. ### ### and lower walls on the sum of the ### ### coordination numbers to keep the ### ### S-S distance below ~0.23 nm ###coord-sum:COMBINECalculate a polynomial combination of a set of other variables. More detailsARG=the input to this functionc1,c2,c3PERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functionLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingcoord-sumAT=1.82the positions of the wallKAPPA=20000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall-coord

### Upper walls on each Coord nr. to ### ### avoid reaction to S-S-S species ###UPPER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingc1,c2,c3AT=1.8,1.8,1.8the positions of the wallKAPPA=50000,50000,50000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsuwall-coord... UPPER_WALLS

### Print dist+coord and wall-bias ###Print quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,c1,c2,c3,coord-sum,lwall-coord.bias,uwall-coord.bias,uwall-dist.bias,lwall-sum_dist.biasSTRIDE=20the frequency with which the quantities of interest should be outputFILE=coord_s-s.datthe name of the file on which to output these quantities

#################### ### Coordination ### ### of CB-atoms ### ####################cys1-coord:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More detailsSPECIESA=2this keyword is used for colvars such as the coordination numberSPECIESB=1,3,4this keyword is used for colvars such as the coordination numberR_0=0.130The r_0 parameter of the switching functionNN=45The n parameter of the switching functionMM=90The m parameter of the switching function; 0 implies 2*NNMEANcalculate the mean of all the quantitiescys2-coord:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More detailsSPECIESA=7this keyword is used for colvars such as the coordination numberSPECIESB=6,8,9this keyword is used for colvars such as the coordination numberR_0=0.130The r_0 parameter of the switching functionNN=45The n parameter of the switching functionMM=90The m parameter of the switching function; 0 implies 2*NNMEANcalculate the mean of all the quantitiescys3-coord:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More detailsSPECIESA=12this keyword is used for colvars such as the coordination numberSPECIESB=11,13,14this keyword is used for colvars such as the coordination numberR_0=0.130The r_0 parameter of the switching functionNN=45The n parameter of the switching functionMM=90The m parameter of the switching function; 0 implies 2*NNMEANcalculate the mean of all the quantitiesLOWER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingcys1-coord.mean,cys2-coord.mean,cys3-coord.meanAT=2.5,2.5,2.5the positions of the wallKAPPA=50000,50000,50000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall-HB... LOWER_WALLS

#################### ### Lower Walls ### ### S - HB ### ####################S1-2HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,6the pair of atom that we are calculating the distance betweenS1-2HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,8the pair of atom that we are calculating the distance betweenS1-2HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,9the pair of atom that we are calculating the distance betweenS1-3HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,11the pair of atom that we are calculating the distance betweenS1-3HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,13the pair of atom that we are calculating the distance betweenS1-3HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,14the pair of atom that we are calculating the distance betweenS2-1HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,1the pair of atom that we are calculating the distance betweenS2-1HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,3the pair of atom that we are calculating the distance betweenS2-1HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,4the pair of atom that we are calculating the distance betweenS2-3HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,11the pair of atom that we are calculating the distance betweenS2-3HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,13the pair of atom that we are calculating the distance betweenS2-3HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,14the pair of atom that we are calculating the distance betweenS3-2HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,6the pair of atom that we are calculating the distance betweenS3-2HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,8the pair of atom that we are calculating the distance betweenS3-2HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,9the pair of atom that we are calculating the distance betweenS3-1HB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,1the pair of atom that we are calculating the distance betweenS3-1HB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,3the pair of atom that we are calculating the distance betweenS3-1HB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,4the pair of atom that we are calculating the distance betweenLOWER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingS1-2HB1,S1-2HB2,S1-2HB3,S1-3HB1,S1-3HB2,S1-3HB3,S2-1HB1,S2-1HB2,S2-1HB3,S2-3HB1,S2-3HB2,S2-3HB3,S3-2HB1,S3-2HB2,S3-2HB3,S3-1HB1,S3-1HB2,S3-1HB3AT=0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3the positions of the wallKAPPA=50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall_S-HB... LOWER_WALLS

#################### ### Lower Walls ### ### S - HB ### ####################S1-CB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,7the pair of atom that we are calculating the distance betweenS1-CB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,12the pair of atom that we are calculating the distance betweenS2-CB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,2the pair of atom that we are calculating the distance betweenS2-CB3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,12the pair of atom that we are calculating the distance betweenS3-CB1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,2the pair of atom that we are calculating the distance betweenS3-CB2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,7the pair of atom that we are calculating the distance betweenLOWER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingS1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2AT=0.3,0.3,0.3,0.3,0.3,0.3the positions of the wallKAPPA=50000,50000,50000,50000,50000,50000the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall_S-CB... LOWER_WALLS

### Print dist+coord and wall-bias ###Print quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsS1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2,lwall_S-CB.bias,lwall_S-HB.biasSTRIDE=100the frequency with which the quantities of interest should be outputFILE=cb-s_hb-s_dist.datthe name of the file on which to output these quantities

##################### ### S-Na distance ### #####################

### CYS1-Na ###nd1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,2650 ### CYS2-Na ###the pair of atom that we are calculating the distance betweennd2:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,2650 ### CYS3-Na ###the pair of atom that we are calculating the distance betweennd3:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,2650the pair of atom that we are calculating the distance between

# Upper Walls distancesLOWER_WALLS...Defines a wall for the value of one or more collective variables, More detailsARG=the arguments on which the bias is actingnd1,nd2,nd3AT=1.2,1.2,1.2the positions of the wallKAPPA=100000.0,100000.0,100000.0the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionslwall-ndist... LOWER_WALLSPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsnd1,nd2,nd3,lwall-ndist.biasSTRIDE=100the frequency with which the quantities of interest should be outputFILE=ndist.datthe name of the file on which to output these quantities

#################### ### Metadynamics ### ####################METAD...Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More detailsLABEL=a label for the action so that its output can be referenced in the input to other actionsmetadARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3HEIGHT=0.5the heights of the Gaussian hillsSIGMA=0.02,0.02,0.02the widths of the Gaussian hillsGRID_MIN=0.15,0.15,0.15the lower bounds for the gridGRID_MAX=0.7,0.7,0.7the upper bounds for the gridGRID_SPACING=0.005,0.005,0.005the approximate grid spacing (to be used as an alternative or together with GRID_BIN)PACE=250the frequency for hill additionBIASFACTOR=20use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsWALKERS_N=24number of walkersWALKERS_ID=0walker idWALKERS_DIRshared directory with the hills files from all the walkersWALKERS_RSTRIDE=500 ... METADstride for reading hills filesPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,metad.bias,cys1-coord.mean,cys2-coord.mean,cys3-coord.mean,lwall-HB.biasSTRIDE=100the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantities