Project ID: plumID:21.018
Source: plumed_metad/metad_35ang_para.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=1-3677the atoms that make up a molecule that you wish to alignENTITY1=3678-3734the 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=../input/MacroD2_para_input/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=../input/MacroD2_para_input/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=../input/MacroD2_para_input/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 definition
Fix:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=5.0,5.0,5.0 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. More detailsARG=abs_z,abs_ythe input to this functionFUNC=(x-y)/sqrt(2the 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 ef CUSTOM function. More detailsARG=abs_xthe input to this functionFUNC=xthe 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 ef CUSTOM function. More detailsARG=abs_z,abs_ythe input to this functionFUNC=(x+y)/sqrt(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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 function
rmsd:RMSDCalculate the RMSD with respect to a reference structure. More detailsREFERENCE=../input/MacroD2_para_input/ref_protein_noH_nosite.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=SIMPLEthe 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 number c:COORDINATIONCalculate coordination numbers. More detailsGROUPA=AR6First list of atomsGROUPB=prot_nohSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.45The r_0 parameter of the switching function
# MetadynamicsMETAD...Used to performed metadynamics on one or more collective variables. 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_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