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
=ixoThe COM action with label ixo calculates the following quantities:
 Quantity   
 Type   
 Description  
ixo
atoms
virtual atom calculated by COM action

# 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
=pktThe COM action with label pkt calculates the following quantities:
 Quantity   
 Type   
 Description  
pkt
atoms
virtual atom calculated by COM action

# 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
=d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms 
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)
d1xThe COMBINE action with label d1x calculates the following quantities:
 Quantity   
 Type   
 Description  
d1x
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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
d1yThe COMBINE action with label d1y calculates the following quantities:
 Quantity   
 Type   
 Description  
d1y
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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
d1zThe COMBINE action with label d1z calculates the following quantities:
 Quantity   
 Type   
 Description  
d1z
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values 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 labels of the scalars on which the bias will act
=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
=rmdThe ABMD action with label rmd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmd.bias
scalar
the instantaneous value of the bias potential
rmd.d1z_min
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file.  These quantities will be named with the arguments of the bias followed by the character string _min. These quantities tell the user the minimum value assumed by rho_m(t). This particular component measures this quantity for the input CV named d1z
rmd.force2
scalar
the instantaneous value of the squared force due to this bias potential
... ABMD


# Here we print all the data regarding rMD_data
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=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
The PRINT action with label  calculates something
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=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