Project ID: plumID:20.025
Source: OAH_alone/plumed.dat
Originally used with PLUMED version: 2.5
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
tested onv2.9
tested onmaster
# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

HOST: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-184      #host atoms
WO: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=193-6492:3    #water oxygen atoms

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=HOST

FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
REFERENCE
a 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

v1: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.0   #virtual atoms
v2: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.25
v3: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.5
v4: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.75
v5: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.0
v6: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.25
v7: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.5
v8: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.75

# --- (2) DESCRIPTORS ---

#V1: COORDINATION GROUPA=v1 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
V2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
#V3: COORDINATION GROUPA=v3 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V4: COORDINATION GROUPA=v4 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V5: COORDINATION GROUPA=v5 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V6: COORDINATION GROUPA=v6 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V7: COORDINATION GROUPA=v7 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5
#V8: COORDINATION GROUPA=v8 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST NL_CUTOFF=1.0 NL_STRIDE=5

# --- (3) DEEP-LDA CV and other quantities ---

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details


# --- (4) OPES  ---

OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes
   
ARG
the input for this action is the scalar output from one or more other actions
=V2
   
FILE
 a file in which the list of all deposited kernels is stored
=Kernels.data
   
PACE
the frequency for kernel deposition
=500
   
BARRIER
the free energy barrier to be overcome
=50
   
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
   
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=compressed_Kernels.data
   
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=compressed_Kernels.data
   
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=50000
   #WALKERS_MPI
... OPES_METAD

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f

ENDPLUMED
Terminate plumed input. More details