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
tested onv2.10
tested onmaster
RESTARTActivate restart. More details
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A # modify the default length unit (nm) to Angstrom

# 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 details ATOMSthe numerical indexes for the set of atoms in the group=1517 K2: 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 details ATOMSthe numerical indexes for the set of atoms in the group=1519 KBULK: 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 details ATOMSthe numerical indexes for the set of atoms in the group=35596,35598,35600,35602,35604,35606,35608,35610,35612,35614,35616,35618,35620,35622,35624,35626,35628,35630,35632,35634,35636,35638,35640,35642,35644,35646,35648,35650,35652,35654 d1: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables d2: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=KBULK LOWEST this flag allows you to recover the lowest of these variables d3: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=K2 LOWEST this 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 details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=5.5 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 lwall2: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2.lowest ATthe positions of the wall=5.5 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 #########################################
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=d1.lowest,d2.lowest,d3.lowest FILEthe name of the file on which to output these quantities=mindist.dat