Project ID: plumID:22.009
Source: plumed.dat
Originally used with PLUMED version: 2.5
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-432 ENTITY1the atoms that make up a molecule that you wish to align=433-442 ENTITY2the atoms that make up a molecule that you wish to align=449-451 ENTITY3the atoms that make up a molecule that you wish to align=452-454 ENTITY4the atoms that make up a molecule that you wish to align=455-457 ENTITY5the atoms that make up a molecule that you wish to align=458-460 ENTITY6the atoms that make up a molecule that you wish to align=461-463 ENTITY7the atoms that make up a molecule that you wish to align=464-466 ENTITY8the atoms that make up a molecule that you wish to align=467-469 ENTITY9the atoms that make up a molecule that you wish to align=470-472

FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

rmsd_cal: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms_cal.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_wat: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms_wat.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_sub: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms_sub.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_all: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms_npt_sel.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

h: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=473,484,485,30,102,123,33,2,120,481,482 o_ph: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=29,101,122,32,119,1 o_w1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=483 o_w2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=480 o_me: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=472 cl: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=455 gly: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=448,447,454,457,458,438,437,440,441,463 d_clo: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=455,480 d_oho: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,483 d_ocl: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,454 d_clc: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=455,454 d_mec: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=472,454 d_hgc: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=456,454 d_hgc2: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=459,458 d_w2ph1: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=o_w2,1 d_w2ph2: DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=o_w2,119 b_clo: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w2 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5} b_oho: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=o_me GROUPB=o_w1 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=1.5} b_clm: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_w1 SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0} b_clg: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=gly SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0} b_clp: BRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms This action is a shortcut. More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=h GROUPA=cl GROUPB=o_ph SWITCHThe parameters of the two switchingfunction in the above formula={RATIONAL R_0=2.0}
c_o_w1h: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=o_w1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5 c_o_meh: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=o_me GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=1.5 c_h_cl: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=cl GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=h R_0The r_0 parameter of the switching function=2.0
diff: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d_clc,d_mec COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #NORMALIZE
prod: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=c_o_w1h,c_o_meh FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO a: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=455,454,472 a1: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=480,455,454 a2: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=454,472,483 dch1: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=464 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=465,466,467 MEAN calculate the mean of all the quantities dch2: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=460 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=461,462 MEAN calculate the mean of all the quantities dch3: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=433 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=435,436,434 MEAN calculate the mean of all the quantities dch4: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=438 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=439 MEAN calculate the mean of all the quantities dch5: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=442 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=445,443,444 MEAN calculate the mean of all the quantities dch6: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=454 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=456 MEAN calculate the mean of all the quantities dch7: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=447 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=453 MEAN calculate the mean of all the quantities dch8: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=449 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=450,451,452 MEAN calculate the mean of all the quantities
dco1: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=454,458 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=457 MEAN calculate the mean of all the quantities dco2: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=464,460 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=463 MEAN calculate the mean of all the quantities dco3: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=433,438 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=437 MEAN calculate the mean of all the quantities dco4: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=440,442 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=441 MEAN calculate the mean of all the quantities dco5: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=447,449 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=448 MEAN calculate the mean of all the quantities

uwall_1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_clo ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=200 uwall_2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_oho ATthe positions of the wall=2.5 KAPPAthe force constant for the wall=200 uwall_6: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_all ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=25000 uwall_7: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=b_clo ATthe positions of the wall=+0.5 KAPPAthe force constant for the wall=700 uwall_8: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=b_oho ATthe positions of the wall=+0.5 KAPPAthe force constant for the wall=700 uwall_10: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=prod ATthe positions of the wall=+2.5 KAPPAthe force constant for the wall=200 uwall_11: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=prod ATthe positions of the wall=+2.0 KAPPAthe force constant for the wall=150 uwall_12: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=+2.5 KAPPAthe force constant for the wall=150 #modifed from +3.5 uwall_13: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=-2.5 KAPPAthe force constant for the wall=200 #modifed from -3.5 uwall_15: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=c_h_cl ATthe positions of the wall=+1.1 KAPPAthe force constant for the wall=300 uwall_16: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=b_clm ATthe positions of the wall=+0.0 KAPPAthe force constant for the wall=700 uwall_17: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=b_clg ATthe positions of the wall=+0.1 KAPPAthe force constant for the wall=700 uwall_18: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=b_clp ATthe positions of the wall=+0.1 KAPPAthe force constant for the wall=700 uwall_19: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_w2ph1 ATthe positions of the wall=+2.4 KAPPAthe force constant for the wall=200 uwall_20: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_w2ph2 ATthe positions of the wall=+2.4 KAPPAthe force constant for the wall=200 uwall_21: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_hgc ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_22: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_hgc2 ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 auwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a ATthe positions of the wall=+2.6281 KAPPAthe force constant for the wall=400 a1uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1 ATthe positions of the wall=+2.0699 KAPPAthe force constant for the wall=400 a2uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a2 ATthe positions of the wall=+1.9018 KAPPAthe force constant for the wall=400 alwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a ATthe positions of the wall=+2.6281 KAPPAthe force constant for the wall=400 a1lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a1 ATthe positions of the wall=+2.0699 KAPPAthe force constant for the wall=400 a2lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=a2 ATthe positions of the wall=+1.9018 KAPPAthe force constant for the wall=400 uwall_dch1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch1.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch2.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch3.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch4: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch4.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch5: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch5.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch6: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch6.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch7: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch7.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dch8: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dch8.mean ATthe positions of the wall=+1.0 KAPPAthe force constant for the wall=200 uwall_dco1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dco1.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200 uwall_dco2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dco2.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200 uwall_dco3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dco3.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200 uwall_dco4: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dco4.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200 uwall_dco5: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dco5.mean ATthe positions of the wall=+1.4 KAPPAthe force constant for the wall=200 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=metad ARGthe labels of the scalars on which the bias will act=diff PACEthe frequency for hill addition=100 HEIGHTthe heights of the Gaussian hills=3.0 SIGMAthe widths of the Gaussian hills=0.05 BIASFACTORuse well tempered metadynamics and use this bias factor=50 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=-9.0 GRID_MAXthe upper bounds for the grid=9 GRID_BINthe number of bins for the grid=200 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] ... METAD
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=diff,d_clo,d_oho,d_ocl,rmsd_cal,rmsd_wat,rmsd_sub,rmsd_all,prod,b_clo,b_oho,b_clm,prod,a,c_h_cl,metad.* FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1