PLUMED-NEST

Project ID: plumID:23.023
Source: silicate_files/plumed.dat
Originally used with PLUMED version: 2.8
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

## RESTART

# Silicate Ions
SIL1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=339-346
The COM action with label SIL1 calculates somethingSIL2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=347-354
The COM action with label SIL2 calculates somethingSIL3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=355-362
The COM action with label SIL3 calculates somethingSIL4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=363-370
The COM action with label SIL4 calculates somethingSIL5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=371-378
The COM action with label SIL5 calculates somethingSIL6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=379-386

# Lysine head groups
The COM action with label SIL6 calculates somethingK1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=48-51
The COM action with label K1 calculates somethingK2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=70-73
The COM action with label K2 calculates somethingK3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=198-201
The COM action with label K3 calculates somethingK4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=247-250

# Arginine head groups
The COM action with label K4 calculates somethingR1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=266-271
The COM action with label R1 calculates somethingR2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=287-292

# Coordination with silicate ions
The COM action with label R2 calculates something
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=K1,K2,K3,K4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=SIL1,SIL2,SIL3,SIL4,SIL5,SIL6 
R_0
The r_0 parameter of the switching function
=0.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
NN
 The n parameter of the switching function 
=20 
MM
 The m parameter of the switching function; 0 implies 2*NN
=40 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=KCN
The COORDINATION action with label KCN calculates the following quantities:
 Quantity   
 Description  
KCN.value
the value of the coordination
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=R1,R2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=SIL1,SIL2,SIL3,SIL4,SIL5,SIL6 
R_0
The r_0 parameter of the switching function
=0.5 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=100 
NN
 The n parameter of the switching function 
=20 
MM
 The m parameter of the switching function; 0 implies 2*NN
=40 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=RCN

# Radius of Gyration: All CA atoms
The COORDINATION action with label RCN calculates the following quantities:
 Quantity   
 Description  
RCN.value
the value of the coordination
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=16,30,52,74,88,101,115,139,153,166,180,202,215,229,251,272,293,312,331  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg

The GYRATION action with label rg calculates something
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
ARG
the input for this action is the scalar output from one or more other actions
=KCN,RCN,rg
SIGMA
the widths of the Gaussian hills
=200.0
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.02,0.02,0.05
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.5,0.5,0.6
HEIGHT
the height of the Gaussian hills, one for all biases
=2.0 #kJ/mol
PACE
the frequency for hill addition, one for all biases
=500
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=16  # Sqrt[cv]*8
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=PBMETAD
GRID_MIN
the lower bounds for the grid
=-0.5,-0.5,-0.5
GRID_MAX
the upper bounds for the grid
=25.0,13.0,15.0
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=../HILLS.KCN,../HILLS.RCN,../HILLS.rg
... PBMETAD

The PBMETAD action with label PBMETAD calculates the following quantities:
 Quantity   
 Description  
PBMETAD.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=KCN,RCN,rg,PBMETAD.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR