Project ID: plumID:22.013
Source: plumed/6e1u/production/plumed.production.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=reference.pdba file in pdb format containing a reference structureMOLTYPE=rnawhat kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
res31:COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@sugar-31res23:the heavy atoms of the sugar in residue 31. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@sugar-23res5:the heavy atoms of the sugar in residue 23. Click here for more information.COMCalculate the center of mass for a group of atoms. More detailsATOMS=the list of atoms which are involved the virtual atom's definition@sugar-5the heavy atoms of the sugar in residue 5. Click here for more information.
res31_l_C07_1070:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=res31,1070 res23_l_C11_1073:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=res23,1073 res5_l_C15_1064:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=res5,1064the pair of atom that we are calculating the distance betweenCOMBINECalculate a polynomial combination of a set of other variables. More detailsLABEL=rc1a label for the action so that its output can be referenced in the input to other actionsARG=res31_l_C07_1070,res23_l_C11_1073,res5_l_C15_1064the input to this functionPOWERS=1,1,1the powers to which you are raising each of the arguments in your functionCOEFFICIENTS=0.8368179798126221,-0.16150334477424622,-0.52311772108078the coefficients of the arguments in your functionPERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
cn:COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More detailsSPECIESA=1063-1099this keyword is used for colvars such as the coordination numberSPECIESB=1-1062this keyword is used for colvars such as the coordination numberNN=4The n parameter of the switching functionR_0=0.3The r_0 parameter of the switching functionMAX={BETA=0.1}calculate the maximum valueMEANcalculate the mean of all the quantities
rmsd1:RMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd1.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd2:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd2.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd3:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd3.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd4:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd4.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd5:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd5.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd6:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd6.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd7:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd7.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd8:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd8.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd9:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd9.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd10:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd10.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd11:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd11.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd12:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd12.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd13:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd13.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd14:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd14.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd15:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd15.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd16:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd16.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd17:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd17.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd18:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd18.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd19:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd19.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd20:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd20.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd21:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd21.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd22:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd22.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd23:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd23.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd24:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd24.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd25:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd25.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd26:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd26.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd27:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd27.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd28:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd28.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd29:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd29.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd30:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd30.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd31:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd31.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd32:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd32.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMAL rmsd33:the manner in which RMSD alignment is performedRMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=PDB/rmsd33.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedCOMMITTOR...Does a committor analysis. More detailsARG=cn.maxthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the CVs are analyzedBASIN_LL1=0.0List of lower limits for basin #BASIN_UL1=1.0 ... COMMITTORList of upper limits for basin #METAD...Used to performed metadynamics on one or more collective variables. More detailsLABEL=metada label for the action so that its output can be referenced in the input to other actionsARG=rc1the input for this action is the scalar output from one or more other actionsSIGMA=0.06the widths of the Gaussian hillsHEIGHT=1.0the heights of the Gaussian hillsBIASFACTOR=10use well tempered metadynamics and use this bias factorTEMP=300.0the system temperature - this is only needed if you are doing well-tempered metadynamicsPACE=2000the frequency for hill additionGRID_MIN=-3.79the lower bounds for the gridGRID_MAX=3.60the upper bounds for the gridGRID_BIN=200the number of bins for the gridCALC_RCT... METADcalculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]Print quantities to a file. More detailsARG=rmsd1,rmsd2,rmsd3,rmsd4,rmsd5,rmsd6,rmsd7,rmsd8,rmsd9,rmsd10,rmsd11,rmsd12,rmsd13,rmsd14,rmsd15,rmsd16,rmsd17,rmsd18,rmsd19,rmsd20,rmsd21,rmsd22,rmsd23,rmsd24,rmsd25,rmsd26,rmsd27,rmsd28,rmsd29,rmsd30,rmsd31,rmsd32,rmsd33the input for this action is the scalar output from one or more other actionsSTRIDE=10the frequency with which the quantities of interest should be outputFILE=6e1u_rmsdthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=res31_l_C07_1070,res23_l_C11_1073,res5_l_C15_1064,cn.max,cn.mean,rc1,metad.bias,metad.rbiasthe input for this action is the scalar output from one or more other actionsSTRIDE=10the frequency with which the quantities of interest should be outputFILE=6e1u_COLVARthe name of the file on which to output these quantities