PLUMED-NEST

Project ID: plumID:22.045
Source: plumed-PULL.dat
Originally used with PLUMED version: 2.4.3
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

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=1-4053          	# all prot and lig complex

The WHOLEMOLECULES action with label  calculates somethingDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1912,4012  LABELa label for the action so that its output can be referenced in the input to other actions=d0The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Type   
 Description  
d0
scalar
the DISTANCE between this pair of atoms      # 130SER-OG lig-C(C=O) C37
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3984,4016  LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms      # extremities lig-C(C=O)
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-3963          LABELa label for the action so that its output can be referenced in the input to other actions=C0The COM action with label C0 calculates the following quantities:
 Quantity   
 Type   
 Description  
C0
atoms
virtual atom calculated by COM action      # prot
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4012,C0    LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
scalar
the DISTANCE between this pair of atoms      # lig C37 vs com
ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1912,C0,4012  LABELa label for the action so that its output can be referenced in the input to other actions=a0The ANGLE action with label a0 calculates the following quantities:
 Quantity   
 Type   
 Description  
a0
scalar
the ANGLE involving these atoms      # 130SER-CA vs com vs lig C37


MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...

  ARGthe labels of the scalars on which the bias will act=a0,d2,d0
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0       AT0ATx is equal to the position of the restraint at time STEPx=0,2.5,0.5            KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=0,0,0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=5000    AT1ATx is equal to the position of the restraint at time STEPx=0,2.5,0.5            KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=5000,5000,0
  STEP2This keyword appears multiple times as STEPx with x=0,1,2,=10000   AT2ATx is equal to the position of the restraint at time STEPx=0,2.5,0.5            KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=5000,5000,0
  STEP3This keyword appears multiple times as STEPx with x=0,1,2,=15000   AT3ATx is equal to the position of the restraint at time STEPx=0,2.5,0.5            KAPPA3KAPPAx is equal to the value of the force constants at time STEPx=5000,0,5000

... MOVINGRESTRAINT

LOWER_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=2.3 KAPPAthe force constant for the wall=250 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=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

PRINTPrint 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=10    FILEthe name of the file on which to output these quantities=COLVAR