Project ID: plumID:23.025
Source: repulsive/3ibk/terra_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
Click on the labels of the actions for more information on what each action computes
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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
# TERRA GQ ######################################### # PDB NUMBERING MUST BE USED HERE # K1 = 1517 (pdb numbering) # K2 = 1519 (pdb numbering) # Kbulk = 35596-35655 (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=1517 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=1519 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=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35634,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654the numerical indexes for the set of atoms in the group
d1:DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. 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 This action is a shortcut. 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 This action is a shortcut. 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 labels of the values that you would like to print to the fileFILE=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 labels of the values that you would like to print to the fileFILE=mindist.datthe name of the file on which to output these quantities