PLUMED-NEST

Project ID: plumID:24.022
Source: OAMe-G4/opes_flooding/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


chi_excThe CUSTOM action with label chi_exc calculates the following quantities:
 Quantity   
 Type   
 Description  
chi_exc
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cyl.z FUNCthe function you wish to evaluate=step(x-0.7) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=cyl.z
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=20
  TEMP temperature=300
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. 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 kernel deposition=500
  BARRIERthe free energy barrier to be overcome=20
  TEMP temperature=300
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...


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,opes.bias 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