PLUMED-NEST-TEST-SITE

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

Click on the labels of the actions for more information on what each action computes

RESTARTActivate restart. More details
The RESTART action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A # modify the default length unit (nm) to Angstrom

# TELOMERE GQ
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# PDB NUMBERING MUST BE USED HERE
# K1 = 1453 (pdb numbering)
# K22 = 1455 (pdb numbering)
# Kbulk = 38392-38473 (remove drude particles from list!) (pdb numbering)
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# 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=1453
The GROUP action with label K1 calculates somethingK2: 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=1455
The GROUP action with label K2 calculates somethingKBULK: 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=38392,38394,38396,38398,38400,38402,38404,38406,38408,38410,38412,38414,38416,38418,38420,38422,38424,38426,38428,38430,38432,38434,38436,38438,38440,38442,38444,38446,38448,38450,38452,38454,38456,38458,38460,38462,38464,38466,38468,38470,38472

The GROUP action with label KBULK calculates somethingd1: DISTANCESCalculate the distances between multiple piars of atoms 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
The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.lowest
the smallest of the colvars
d1.value
the DISTANCES between the each pair of atoms that were specifiedd2: DISTANCESCalculate the distances between multiple piars of atoms 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
The DISTANCES action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.lowest
the smallest of the colvars
d2.value
the DISTANCES between the each pair of atoms that were specifiedd3: DISTANCESCalculate the distances between multiple piars of atoms 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

The DISTANCES action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.lowest
the smallest of the colvars
d3.value
the DISTANCES between the each pair of atoms that were specifiedlwall1: 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
The LOWER_WALLS action with label lwall1 calculates the following quantities:
 Quantity   
 Description  
lwall1.bias
the instantaneous value of the bias potential
lwall1.force2
the instantaneous value of the squared force due to this bias potentiallwall2: 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
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The LOWER_WALLS action with label lwall2 calculates the following quantities:
 Quantity   
 Description  
lwall2.bias
the instantaneous value of the bias potential
lwall2.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint 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