Project ID: plumID:23.040
Source: plumed_analysis/pyrogallolarene/plumed_solvent.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=1 #Amstroeng, hartree, fsthe units of timeWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-76the atoms that make up a molecule that you wish to alignENTITY1=77-152the atoms that make up a molecule that you wish to alignENTITY2=153-228the atoms that make up a molecule that you wish to alignENTITY3=229-304the atoms that make up a molecule that you wish to alignENTITY4=305-380the atoms that make up a molecule that you wish to alignENTITY5=381-456the atoms that make up a molecule that you wish to align
# Group definition cal1: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 detailsATOMS=1-76 cal2:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=77-152 cal3:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=153-228 cal4:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=229-304 cal5:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=305-380 cal6:the numerical indexes for the set of atoms in the groupGROUPDefine 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 detailsATOMS=381-456the numerical indexes for the set of atoms in the group
cl3_com: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=index_files/com_cl3.ndxthe name of index file (gromacs syntax)NDX_GROUP=CL3_COMthe name of the group to be imported (gromacs syntax) - first group found is used by default
com1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal1 com2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal2 com3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal3 com4:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal4 com5:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal5 com6:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal6the group of atoms that you are calculating the Gyration Tensor for
com_all:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=cal1,cal2,cal3,cal4,cal5,cal6the group of atoms that you are calculating the Gyration Tensor forDISTANCES...Calculate the distances between multiple piars of atoms More detailsLABEL=inside_mola label for the action so that its output can be referenced in the input to other actionsGROUPA=com_allCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=cl3_comCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLESS_THAN={RATIONAL R_0=6.5} ... DISTANCEScalculate the number of variables that are less than a certain target valuePrint quantities to a file. More detailsARG=inside_molthe input for this action is the scalar output from one or more other actionsFILE=solvent.datthe name of the file on which to output these quantitiesSTRIDE=1the 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=1the frequency with which all the open files should be flushed