Project ID: plumID:21.018
Source: input/MacroD2_Y190N_input/metad_35ang.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-3670the atoms that make up a molecule that you wish to alignENTITY1=3671-3727the atoms that make up a molecule that you wish to align
# Group definition prot_noh: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 detailsNDX_FILE=ref_index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Protein-H ref:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=ref_index.ndxthe name of index file (gromacs syntax)NDX_GROUP=Prot_ref_noH AR6:the name of the group to be imported (gromacs syntax) - first group found is used by defaultGROUPDefine 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 detailsNDX_FILE=ref_index.ndxthe name of index file (gromacs syntax)NDX_GROUP=AR6_noHthe name of the group to be imported (gromacs syntax) - first group found is used by default
ref_center:COMCalculate the center of mass for a group of atoms. More detailsATOMS=ref AR6_center:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=AR6the list of atoms which are involved the virtual atom's definitionFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=5.0,5.0,5.0 Fix: Dis:coordinates of the virtual atomDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=ref_center,Fixthe pair of atom that we are calculating the distance between
ref_coord:POSITIONCalculate the components of the position of an atom. More detailsATOM=ref_centerthe atom numberNOPBCAR6_coord:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=AR6_centerthe atom numberNOPBCignore the periodic boundary conditions when calculating distances
abs_x:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=AR6_coord.x,ref_coord.xthe input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NO abs_y:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=AR6_coord.y,ref_coord.ythe input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NO abs_z:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=AR6_coord.z,ref_coord.zthe input to this functionFUNC=x-ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
rel_x:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_zthe input to this functionFUNC=xthe function you wish to evaluatePERIODIC=NO rel_y:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,abs_ythe input to this functionFUNC=(sqrt(3)*y+x)/2the function you wish to evaluatePERIODIC=NO rel_z:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,abs_ythe input to this functionFUNC=(y-sqrt(3)*x)/2the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
rho:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=abs_x,abs_y,abs_zthe input to this functionFUNC=sqrt(x*x+y*y+z*zthe function you wish to evaluatePERIODIC=NO siga:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=rel_z,rhothe input to this functionFUNC=sqrt(-x+ythe function you wish to evaluatePERIODIC=NO theta:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=rel_x,rel_ythe input to this functionFUNC=atan2(y,xthe function you wish to evaluatePERIODIC=-pi,piif the output of your function is periodic then you should specify the periodicity of the functionRMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More detailsREFERENCE=ref_protein_noH_nosite.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=SIMPLE rmsd:the manner in which RMSD alignment is performed
# Restraining potential of the sphere restr_dis:UPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=Disthe arguments on which the bias is actingAT=1.00the positions of the wallKAPPA=20000the force constant for the wallOFFSET=0 restr_rho:the offset for the start of the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rhothe arguments on which the bias is actingAT=3.50the positions of the wallKAPPA=20000the force constant for the wallOFFSET=0 restr_siga:the offset for the start of the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=sigathe arguments on which the bias is actingAT=1.0the positions of the wallKAPPA=20000the force constant for the wallOFFSET=0 restr_rmsd:the offset for the start of the wallUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsdthe arguments on which the bias is actingAT=0.10the positions of the wallKAPPA=20000the force constant for the wallOFFSET=0the offset for the start of the wall
# Coordination numberCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More detailsGROUPA=AR6First list of atomsGROUPB=prot_nohSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.45 c:The r_0 parameter of the switching function
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More detailsARG=rho,siga,thetathe input for this action is the scalar output from one or more other actionsGRID_MIN=0,0,-pithe lower bounds for the gridGRID_MAX=3.6,1.2,pithe upper bounds for the gridSIGMA=0.1,0.04,pi/8the widths of the Gaussian hillsHEIGHT=1.2the heights of the Gaussian hillsPACE=500the frequency for hill additionBIASFACTOR=20use well tempered metadynamics and use this bias factorTEMP=298the system temperature - this is only needed if you are doing well-tempered metadynamicsLABEL=metada label for the action so that its output can be referenced in the input to other actionsCALC_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=metadthe input for this action is the scalar output from one or more other actionsFILE=metad_data.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=restr_dis.*,restr_rho.*,restr_siga.*,restr_rmsdthe input for this action is the scalar output from one or more other actionsFILE=sphere_restraint.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=ref_coord.x,ref_coord.y,ref_coord.zthe input for this action is the scalar output from one or more other actionsFILE=ref_coord.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=AR6_coord.x,AR6_coord.y,AR6_coord.zthe input for this action is the scalar output from one or more other actionsFILE=AR6_coord.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=rho,siga,thetathe input for this action is the scalar output from one or more other actionsFILE=rtp_coord.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=cthe input for this action is the scalar output from one or more other actionsFILE=all_coordination_45.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=rmsdthe input for this action is the scalar output from one or more other actionsFILE=rmsd.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=Disthe input for this action is the scalar output from one or more other actionsFILE=distance.datthe name of the file on which to output these quantitiesSTRIDE=5000the frequency with which the quantities of interest should be outputFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=5000the frequency with which all the open files should be flushed