Project ID: plumID:23.014
Source: CXCR4_dimer/plumed_CXCR4_dimer.dat
Originally used with PLUMED version: 2.3
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 detailsSTRIDE=1the frequency with which molecules are reassembledENTITY0=62,131,132,220,222,226,230,232,324,418,517,521,526,622,634the atoms that make up a molecule that you wish to alignENTITY1=718,787,788,876,878,882,886,888,980,1074,1173,1177,1182,1278,1290the atoms that make up a molecule that you wish to align
comA:COMCalculate the center of mass for a group of atoms. More detailsATOMS=554,558 comB:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=21,162,181,345,400,552,603 comC:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=733,775,898,958,1102,1166,1300 comD:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=955,958 com1:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=62,131,132,220,222,226,230,232,324,418,517,521,526,622,634 com2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=718,787,788,876,878,882,886,888,980,1074,1173,1177,1182,1278,1290 d:the list of atoms which are involved the virtual atom's definitionDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=com1,com2the pair of atom that we are calculating the distance betweenCOMPONENTSdd:calculate the x, y and z components of the distance separately and store them as labelCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=d.x,d.ythe input to this functionPOWERS=2,2the powers to which you are raising each of the arguments in your functionPERIODIC=NO d2:if the output of your function is periodic then you should specify the periodicity of the functionCOMBINECalculate a polynomial combination of a set of other variables. More detailsARG=ddthe input to this functionPOWERS=0.5the powers to which you are raising each of the arguments in your functionPERIODIC=NO torsion:if the output of your function is periodic then you should specify the periodicity of the functionTORSIONCalculate a torsional angle. More detailsATOMS=comA,comB,comC,comDthe four atoms involved in the torsional angle
m:METADUsed to performed metadynamics on one or more collective variables. More detailsARG=d2,torsionthe input for this action is the scalar output from one or more other actionsSIGMA=0.04,0.06the widths of the Gaussian hillsHEIGHT=0.5the heights of the Gaussian hillsPACE=5000the frequency for hill additionBIASFACTOR=20use well tempered metadynamics and use this bias factorTEMP=300the system temperature - this is only needed if you are doing well-tempered metadynamicsGRID_MIN=1.3,-pithe lower bounds for the gridGRID_MAX=8.5,pithe upper bounds for the gridGRID_WFILE=GRID_W.datthe file on which to write the gridGRID_WSTRIDE=1000000write the grid to a file every N stepsWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d2the arguments on which the bias is actingAT=8.0the positions of the wallKAPPA=5000000.0the force constant for the wallEXP=2.0the powers for the wallsOFFSET=0the offset for the start of the wallLABEL=uwallia label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=d2,torsionthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000000the frequency with which all the open files should be flushed