PLUMED-NEST

Project ID: plumID:24.022
Source: OAMe-G4/infr_metad/template/plumed.dat
Originally used with PLUMED version: 2.9
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

# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

HOSTThe GROUP action with label HOST calculates the following quantities:
 Quantity   
 Type   
 Description  
HOST
atoms
indices of atoms specified in GROUP: 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=29-224      #host atoms
LIGCThe GROUP action with label LIGC calculates the following quantities:
 Quantity   
 Type   
 Description  
LIGC
atoms
indices of atoms specified in GROUP: 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=1-11  #carbon atoms in the ligand

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=HOST
The WHOLEMOLECULES action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=conf_template.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL #coordinates alignment
ligThe CENTER_FAST action with label lig calculates the following quantities:
 Quantity   
 Type   
 Description  
lig
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=LIGC

v1The FIXEDATOM action with label v1 calculates the following quantities:
 Quantity   
 Type   
 Description  
v1
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0   #virtual atoms
v1: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0   #virtual atoms  SET_MASS=1 SET_CHARGE=0
v3The FIXEDATOM action with label v3 calculates the following quantities:
 Quantity   
 Type   
 Description  
v3
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5
v3: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
v5The FIXEDATOM action with label v5 calculates the following quantities:
 Quantity   
 Type   
 Description  
v5
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0
v5: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0


angThe ANGLE action with label ang calculates the following quantities:
 Quantity   
 Type   
 Description  
ang
scalar
the ANGLE involving these atoms: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=v3,v5,6,11   #angle of a ligand's axis with z
cosangThe MATHEVAL action with label cosang calculates the following quantities:
 Quantity   
 Type   
 Description  
cosang
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=ang FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

cylThe DISTANCE action with label cyl calculates the following quantities:
 Quantity   
 Type   
 Description  
cyl.x
scalar
the x-component of the vector connecting the two atoms
cyl.y
scalar
the y-component of the vector connecting the two atoms
cyl.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=v1,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label
radiusThe MATHEVAL action with label radius calculates the following quantities:
 Quantity   
 Type   
 Description  
radius
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cyl.x,cyl.y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


#funnel: MATHEVAL ARG=radius,cyl.z VAR=r,z FUNC=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODIC=NO
#UPPER_WALLS AT=0 ARG=funnel KAPPA=2000.0 LABEL=funnelwall  #funnel restraint
#UPPER_WALLS AT=1.8 ARG=cyl.z KAPPA=4000.0 EXP=2 LABEL=upper_wall  #upper limit of cyl.z



metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=cyl.z
  PACEthe frequency for hill addition=10000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=0
  GRID_MAXthe upper bounds for the grid=3.0
  GRID_BINthe number of bins for the grid=150
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] 
...
metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=cyl.z
  PACEthe frequency for hill addition=10000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=0
  GRID_MAXthe upper bounds for the grid=3.0
  GRID_BINthe number of bins for the grid=150
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] 
 FILE a file in which the list of added hills is stored=HILLS
...


COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=cyl.z
 STRIDE the frequency with which the CVs are analyzed=100
 BASIN_LL1List of lower limits for basin #=1.6
 BASIN_UL1List of upper limits for basin #=3.0
... COMMITTOR

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,cosang,metad.* 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 FMTthe format that should be used to output real numbers=%8.4f

ENDPLUMEDTerminate plumed input. More details