PLUMED-NEST-TEST-SITE

Project ID: plumID:24.022
Source: OAMe-G4/integrated_sampling/gromacs_config/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

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

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=500000
  BARRIERthe free energy barrier to be overcome=20
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  FILE a file in which the list of all deposited kernels is stored=KERNELS
...
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=500000
  BARRIERthe free energy barrier to be overcome=20
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  FILE a file in which the list of all deposited kernels is stored=KERNELS
 TEMP temperature=-1 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,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