PLUMED-NEST

Project ID: plumID:25.029
Source: ./PET_extr/eq2_amor.dat
Originally used with PLUMED version: 2.8
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

#RESTART
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-180 # UNK1 UNK2

The WHOLEMOLECULES action with label  calculates somethingCOMCalculate the center of mass for a group of atoms. More details         LABELa label for the action so that its output can be referenced in the input to other actions=c1    ATOMSthe list of atoms which are involved the virtual atom's definition=1-90   #NOPBC   # UNK1 COM
The COM action with label c1 calculates somethingCOMCalculate the center of mass for a group of atoms. More details         LABELa label for the action so that its output can be referenced in the input to other actions=c2    ATOMSthe list of atoms which are involved the virtual atom's definition=91-180   #NOPBC   # UNK2 COM
The COM action with label c2 calculates somethingFIXEDATOMAdd a virtual atom in a fixed position. More details   LABELa label for the action so that its output can be referenced in the input to other actions=gc    ATcoordinates of the virtual atom=6.37671,6.37671,4.50901                     # geometrical center of the box
The FIXEDATOM action with label gc calculates somethingDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d0    ATOMSthe pair of atom that we are calculating the distance between=c1,c2             #NOPBC   # COMs distance MTD CV
The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Description  
d0.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d1    ATOMSthe pair of atom that we are calculating the distance between=21,53     #NOPBC   # UNK1 C17 vs C39
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d2    ATOMSthe pair of atom that we are calculating the distance between=111,143     #NOPBC   # UNK2 C17 vs C39
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d3    ATOMSthe pair of atom that we are calculating the distance between=gc,c1             #NOPBC   # UNK1 COM and geo centre
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details    LABELa label for the action so that its output can be referenced in the input to other actions=d4    ATOMSthe pair of atom that we are calculating the distance between=gc,c2             #NOPBC   # UNK2 COM and geo centre

#metad: METAD ...
#
#    ARG=d0
#    SIGMA=0.05      # 0.5*fluctuation ~ 1A
#    HEIGHT=0.5      # standard ~0.1-1.0*kBT KJ/mol | ~0.02-1.20 d, ~1.0-2.0 a -> TAU??? | from rep0
#    PACE=500        # ~100-500 steps relax system before next hill add
#    BIASFACTOR=15   # barriers 20-30 KJ/mol need a bias factor of ~10-15 biol syst
#    TEMP=300        # well-tempered
#
#...

#   UPPER_WALLS ARG=d0 AT=1.0 KAPPA=1000  EXP=2 EPS=1 OFFSET=0 LABEL=uwall0             # limits grid max
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3 ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=1000  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 LABELa label for the action so that its output can be referenced in the input to other actions=uwall3             # limits grid max
#   UPPER_WALLS ARG=d4 AT=1.0 KAPPA=1000  EXP=2 EPS=1 OFFSET=0 LABEL=uwall4             # limits grid max
The UPPER_WALLS action with label uwall3 calculates the following quantities:
 Quantity   
 Description  
uwall3.bias
the instantaneous value of the bias potential
uwall3.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=2.4 KAPPAthe force constant for the wall=2250  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 LABELa label for the action so that its output can be referenced in the input to other actions=lwall1             # amorphous stretch
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 potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=2.4 KAPPAthe force constant for the wall=2250  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 LABELa label for the action so that its output can be referenced in the input to other actions=lwall2             # amorphous stretch

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 ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500    FILEthe name of the file on which to output these quantities=colvar.eq2                                               #print less