PLUMED-NEST

Project ID: plumID:24.001
Source: amylase/opes_flooding_qmmm/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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A

The UNITS action with label  calculates somethingd_nuc: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=3026,7700
The DISTANCE action with label d_nuc calculates the following quantities:
 Quantity   
 Description  
d_nuc.value
the DISTANCE between this pair of atomsd_gly: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7700,7699
The DISTANCE action with label d_gly calculates the following quantities:
 Quantity   
 Description  
d_gly.value
the DISTANCE between this pair of atomsd_acid: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7699,3607


###### Walls #####################
The DISTANCE action with label d_acid calculates the following quantities:
 Quantity   
 Description  
d_acid.value
the DISTANCE between this pair of atoms
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
=d_nuc 
AT
the positions of the wall
=+4.0 
KAPPA
the force constant for the wall
=500.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_d_nuc
The UPPER_WALLS action with label uwall_d_nuc calculates something
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
=d_acid 
AT
the positions of the wall
=+4.0 
KAPPA
the force constant for the wall
=500.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_d_acid

The UPPER_WALLS action with label uwall_d_acid calculates somethingd_gly-wat: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7699,26287
The DISTANCE action with label d_gly-wat calculates the following quantities:
 Quantity   
 Description  
d_gly-wat.value
the DISTANCE between this pair of atoms
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
=d_gly-wat 
AT
the positions of the wall
=+4.0 
KAPPA
the force constant for the wall
=500.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall_d_gly-wat

#d_strHbond1: DISTANCE ATOMS=7704,4655
#UPPER_WALLS ARG=d_strHbond1 AT=+2.5 KAPPA=1000.0 EXP=2 LABEL=uwall_d_strHbond1
#d_strHbond2: DISTANCE ATOMS=7708,4654
#UPPER_WALLS ARG=d_strHbond2 AT=+2.5 KAPPA=1000.0 EXP=2 LABEL=uwall_d_strHbond2
##################################


#metad: METAD ARG=d_gly SIGMA=0.1 HEIGHT=2.0 PACE=100 

The UPPER_WALLS action with label uwall_d_gly-wat calculates somethingchi_exc: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=d_gly 
FUNC
the function you wish to evaluate
=step(x-1.8 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The CUSTOM action with label chi_exc calculates somethingopes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=d_gly,d_acid
  
PACE
the frequency for kernel deposition
=100
  
ADAPTIVE_SIGMA_STRIDE
number of steps for measuring adaptive sigma
=200
  
BARRIER
the free energy barrier to be overcome
=50
  
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
  
TEMP
 temperature
=300.0
...

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
COMMITTOR
Does a committor analysis. More details
 ...
 
ARG
the input for this action is the scalar output from one or more other actions
=d_gly
 
STRIDE
 the frequency with which the CVs are analyzed
=10
 
BASIN_LL1
List of lower limits for basin #
=3.3
 
BASIN_UL1
List of upper limits for basin #
=10.0
... COMMITTOR


PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d_gly,d_acid,opes.*,uwall_d_nuc.*,uwall_d_acid.*,uwall_d_gly-wat 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=COLVAR

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1