PLUMED-NEST

Project ID: plumID:20.005
Source: input_data/classical/ratchet/rMD_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

#
# This is the input file needed to perform Ratchet&Pawl MD simulation
# based on the CV given by the distance between the ligand's center 
# of mass and the center of the binding pocket.
#
# This input file can be used with all the PLUMED versions >=2.5
#

# Definition of the center of mass of the ligand, considering only its heavy atoms
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
=1,5,6,10,14,17,18,19,22,23,24,25,26,29  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ixo

# Definition of the center of mass of the pocket
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
=1396,1398,1400,1403,1404,1406,1408,1409,1411,1413,1415,1416,1449,1451,1453,1456,1458,1459,1495,1497,1499,1501,1505,1509,1510,2838,2840,2842,2845,2846,2848,2850,2852,2854,2856,2857,3605,3607,3609,3612,3613,3615,3617,3618,3620,3622,3624,3625 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pkt

# Definition of the distance between the ligand and the pocket as a 3d vector xyz
# (the membrane is in the plane xy)
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ixo,pkt 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# Definition of the periodicity of the components of the distance 
# (to avoid jumps in the variable during the simulation due to the 
# rototranslation of the system)
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atomsd1x: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1.x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-4.7,4.7
d1y: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1.y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-4.7,4.7
d1z: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1.z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-8.2,8.2

# Activation of the Ratchet&Pawl MD, to observe the transition of the ligand. 
# Starting from the bound structure, the bias will move the system outside 
# the binding cavity with a k=100 kJ/mol/nm until the ligand is 4 nm outside
# the binding cavity 
ABMD
Adds a ratchet-and-pawl like restraint on one or more variables. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=d1z
  
TO
The array of target values
=-4.0
  
KAPPA
The array of force constants
=100.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rmd
... ABMD


# Here we print all the data regarding rMD_data
The ABMD action with label rmd calculates the following quantities:
 Quantity   
 Description  
rmd.bias
the instantaneous value of the bias potential
rmd.force2
the instantaneous value of the squared force due to this bias potential
rmd._min
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rmd 
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
=rMD_data
# Here we print the distance between the molecule and the binding pocket
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1z 
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
=IXO_dist.dat

ENDPLUMED
Terminate plumed input. More details