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

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
# 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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,10 ### CYS1-CYS3 ### d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15 ### CYS2-CYS3 ### d3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,15 # Upper Walls distances UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=d1,d2,d3 ATthe positions of the wall=0.6,0.6,0.6 KAPPAthe force constant for the wall=100000.0,100000.0,100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=uwall-dist ... UPPER_WALLS
sum_dist: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=sum_dist ATthe positions of the wall=0.9 KAPPAthe force constant for the wall=100000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall-sum_dist ... LOWER_WALLS
######################### ### S-S COORDINATION ### ### and WALLS ### #########################
### S1 Coord ### c1: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=10,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20 ### S2 Coord ### c2: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5,15 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20 ### S3 Coord ### c3: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=15 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5,10 R_0The r_0 parameter of the switching function=0.290 NN The n parameter of the switching function =10 MM The m parameter of the switching function; 0 implies 2*NN=20
### 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 details ARGthe values input to this function=c1,c2,c3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=coord-sum ATthe positions of the wall=1.82 KAPPAthe force constant for the wall=20000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall-coord
### Upper walls on each Coord nr. to ### ### avoid reaction to S-S-S species ### UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=c1,c2,c3 ATthe positions of the wall=1.8,1.8,1.8 KAPPAthe force constant for the wall=50000,50000,50000 LABELa label for the action so that its output can be referenced in the input to other actions=uwall-coord ... UPPER_WALLS
### Print dist+coord and wall-bias ### PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,c1,c2,c3,coord-sum,lwall-coord.bias,uwall-coord.bias,uwall-dist.bias,lwall-sum_dist.bias STRIDE the frequency with which the quantities of interest should be output=20 FILEthe name of the file on which to output these quantities=coord_s-s.dat #################### ### 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 details SPECIESAthe list of atoms for which the symmetry function is being calculated=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1,3,4 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities cys2-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 details SPECIESAthe list of atoms for which the symmetry function is being calculated=7 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=6,8,9 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities cys3-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 details SPECIESAthe list of atoms for which the symmetry function is being calculated=12 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=11,13,14 R_0The r_0 parameter of the switching function=0.130 NN The n parameter of the switching function =45 MM The m parameter of the switching function; 0 implies 2*NN=90 MEAN calculate the mean of all the quantities
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=cys1-coord.mean,cys2-coord.mean,cys3-coord.mean ATthe positions of the wall=2.5,2.5,2.5 KAPPAthe force constant for the wall=50000,50000,50000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall-HB ... LOWER_WALLS
#################### ### Lower Walls ### ### S - HB ### ####################
S1-2HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6 S1-2HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,8 S1-2HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9 S1-3HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,11 S1-3HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,13 S1-3HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,14 S2-1HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1 S2-1HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,3 S2-1HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,4 S2-3HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,11 S2-3HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,13 S2-3HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,14 S3-2HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,6 S3-2HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,8 S3-2HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,9 S3-1HB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,1 S3-1HB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,3 S3-1HB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,4 LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=S1-2HB1,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,S3-1HB3 ATthe positions of the wall=0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3,0.3 KAPPAthe force constant for the wall=50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000,50000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall_S-HB ... LOWER_WALLS
#################### ### Lower Walls ### ### S - HB ### ####################
S1-CB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7 S1-CB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,12 S2-CB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2 S2-CB3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,12 S3-CB1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,2 S3-CB2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,7 LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2 ATthe positions of the wall=0.3,0.3,0.3,0.3,0.3,0.3 KAPPAthe force constant for the wall=50000,50000,50000,50000,50000,50000 LABELa label for the action so that its output can be referenced in the input to other actions=lwall_S-CB ... LOWER_WALLS
### Print dist+coord and wall-bias ### PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=S1-CB2,S1-CB3,S2-CB1,S2-CB3,S3-CB1,S3-CB2,lwall_S-CB.bias,lwall_S-HB.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=cb-s_hb-s_dist.dat ##################### ### S-Na distance ### #####################
### CYS1-Na ### nd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,2650 ### CYS2-Na ### nd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,2650 ### CYS3-Na ### nd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,2650 # Upper Walls distances LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ... ARGthe arguments on which the bias is acting=nd1,nd2,nd3 ATthe positions of the wall=1.2,1.2,1.2 KAPPAthe force constant for the wall=100000.0,100000.0,100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=lwall-ndist ... LOWER_WALLS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=nd1,nd2,nd3,lwall-ndist.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=ndist.dat #################### ### Metadynamics ### #################### METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=metad ARGthe labels of the scalars on which the bias will act=d1,d2,d3 HEIGHTthe heights of the Gaussian hills=0.5 SIGMAthe widths of the Gaussian hills=0.02,0.02,0.02 GRID_MINthe lower bounds for the grid=0.15,0.15,0.15 GRID_MAXthe upper bounds for the grid=0.7,0.7,0.7 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.005,0.005,0.005 PACEthe frequency for hill addition=250 BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 WALKERS_Nnumber of walkers=24 WALKERS_IDwalker id=0 WALKERS_DIRshared directory with the hills files from all the walkers=../ WALKERS_RSTRIDEstride for reading hills files=500 ... METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,metad.bias,cys1-coord.mean,cys2-coord.mean,cys3-coord.mean,lwall-HB.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=colvar