Project ID: plumID:23.025
Source: repulsive/1k8p/telomere_repulsive.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
RESTARTActivate restart. More detailsUNITSThis command sets the internal units for the code. More detailsLENGTH=A # modify the default length unit (nm) to Angstromthe units of lengths
# TELOMERE GQ ######################################### # PDB NUMBERING MUST BE USED HERE # K1 = 1453 (pdb numbering) # K22 = 1455 (pdb numbering) # Kbulk = 38392-38473 (remove drude particles from list!) (pdb numbering) #########################################
######################################### # Defining groups and lower_walls K1: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=1453 K2: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=1455 KBULK: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=38392,38394,38396,38398,38400,38402,38404,38406,38408,38410,38412,38414,38416,38418,38420,38422,38424,38426,38428,38430,38432,38434,38436,38438,38440,38442,38444,38446,38448,38450,38452,38454,38456,38458,38460,38462,38464,38466,38468,38470,38472the numerical indexes for the set of atoms in the group
d1:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=K1Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=KBULKCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLOWESTd2:this flag allows you to recover the lowest of these variablesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=K2Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=KBULKCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLOWESTd3:this flag allows you to recover the lowest of these variablesDISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=K1Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=K2Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPBLOWESTthis flag allows you to recover the lowest of these variables
lwall1:LOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d1.lowestthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0 lwall2:the offset for the start of the wallLOWER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=d2.lowestthe arguments on which the bias is actingAT=5.5the positions of the wallKAPPA=2000.0the force constant for the wallEXP=2the powers for the wallsEPS=1the values for s_i in the expression for a wallOFFSET=0 #########################################the offset for the start of the wallPrint quantities to a file. More detailsSTRIDE=1000the frequency with which the quantities of interest should be outputARGthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsSTRIDE=1000the frequency with which the quantities of interest should be outputARG=d1.lowest,d2.lowest,d3.lowestthe input for this action is the scalar output from one or more other actionsFILE=mindist.datthe name of the file on which to output these quantities