Project ID: plumID:21.027
Source: L858R/plumed.dat
Originally used with PLUMED version: 2.4
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
#RESTART

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=L858R_active.pdb 

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
=1-4722

# Distances describing the two saltbridges K745(NZ):E762(CD) and K745(ΝΖ):D855(CG)
# that reflect the conformation of the aC helix
# (CVs described in Ludo's paper doi:10.1073/pnas.1221953110)

K745_E762: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=745,1078
K745_D855: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=745,2521

# Distance between the two distance
# When both saltbridges are formed, the distance between the two distances (CV)
# is close to 0. This CV is able to characterise the displacement of the fuctionally important
# E762 located in the aC helix of the N-lobe in its transition from the so-called "aC-in" to "aC-out" conformation

MATHEVAL
An alias to the 
ef CUSTOM function. More details
 ...
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d
    
ARG
the input to this function
=K745_E762,K745_D855
    
VAR
the names to give each of the arguments in the function
=a,b
    
FUNC
the function you wish to evaluate
=a-b
    
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... MATHEVAL

# Distance from active cmap

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=cmap_active.dat

# Distance form inactive cmap

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=cmap_inactive.dat
# Confine the explored space
lwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d 
AT
the positions of the wall
=-1.5 
KAPPA
the force constant for the wall
=4000.0
uwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=cmap_active,cmap_inactive,d 
AT
the positions of the wall
=65,65,2.5 
KAPPA
the force constant for the wall
=3500.0,3500.0,4000.0

# Gaussians from an initial metaD sim where the energy was biased
# will be loaded to perform the second metaD in the WTE
ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details


METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=wte
    
ARG
the input for this action is the scalar output from one or more other actions
=ene 
PACE
the frequency for hill addition
=1000000 
HEIGHT
the heights of the Gaussian hills
=2 
SIGMA
the widths of the Gaussian hills
=1100 # Deposit a Gaussian to the potential energy every 2 ns
    
FILE
 a file in which the list of added hills is stored
=HILLS_PTWE 
    
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=
@replicas:
This keyword specifies that different replicas have different values for this quantity.  See here for more details.
300,305,310,318,326,335,344,354,363,375,382
... METAD

# Activate metaD on the rest of the CVs

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=meta
    
ARG
the input for this action is the scalar output from one or more other actions
=cmap_active,cmap_inactive,d 
HEIGHT
the heights of the Gaussian hills
=3.0 
SIGMA
the widths of the Gaussian hills
=0.5,0.5,0.15 
PACE
the frequency for hill addition
=500 
    
GRID_MIN
the lower bounds for the grid
=0,0,-2 
GRID_MAX
the upper bounds for the grid
=70,70,3 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.25,0.25,0.075 
    
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=
@replicas:
This keyword specifies that different replicas have different values for this quantity.  See here for more details.
300,305,310,318,326,335,344,354,363,375,382
... 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
=500 
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