Project ID: plumID:20.000
Source: funnel_metad/funnel_metad_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
tested onv2.9
tested onmaster
#
# This is the input file needed to perform funnel metadynamics simulation
# based on the MC-HLDA CVs 
#
# This input file can be used with all the PLUMED versions >=2.3
#

# 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) d1x:
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
# We define the radius of the funnel potential on the xy plane (the same of the membrane) radius:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=d1x,d1y
VAR
the names to give each of the arguments in the function
=x,y
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO # We define the conical and the cylindrical part of the funnel potential funnel:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG
the input to this function
=radius,d1z
VAR
the names to give each of the arguments in the function
=r,z
FUNC
the function you wish to evaluate
=(r-(z+1.8))*step(z+1.7)+(r-0.1)*step(-1.7-z
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO # We define the funnel potential
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
AT
the positions of the wall
=0
ARG
the arguments on which the bias is acting
=funnel
KAPPA
the force constant for the wall
=2000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnelwall
# Wall on distance to prevent the ligand exit to the solvent
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
AT
the positions of the wall
=-4.0
ARG
the arguments on which the bias is acting
=d1.z
KAPPA
the force constant for the wall
=2000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=topwall # Wall on distance to prevent the ligand entering the intracellular part
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
AT
the positions of the wall
=0.3
ARG
the arguments on which the bias is acting
=d1.z
KAPPA
the force constant for the wall
=2000.0
LABEL
a label for the action so that its output can be referenced in the input to other actions
=bottomwall
# Contact related to the nonbonded interactions in bound state bound_d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=25,3637 bound_d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,3637 bound_d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=25,2842 bound_d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=26,2837 bound_d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,3620 bound_d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=26,1505 bound_d7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=17,1398
# Contact related to the nonbonded interactions in state A cl2_d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=25,1409 cl2_d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,1409 cl2_d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,1456 cl2_d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,1411 cl2_d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=19,3622 cl2_d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,1408
# Contact related to the nonbonded interactions in state B cl3_d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,1404 cl3_d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,3975 cl3_d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=10,1413 cl3_d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,3613
# Contact related to the nonbonded interactions in state C cl5_d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,3618 cl5_d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=25,3618 cl5_d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=23,3615 cl5_d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=29,2791
# Salt bridges sb_d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,1392 sb_d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,1393
# Eigenvectors from the MC-HLDA analysis on the contacts eig1:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2
COEFFICIENTS
the coefficients of the arguments in your function
=0.312,-0.262,0.116,0.021,0.411,0.020,0.073,0.484,-0.490,0.004,0.007,-0.008,-0.002,-0.037,-0.009,-0.001,0.085,-0.054,-0.347,-0.153,0.124,-0.022,-0.012
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO eig2:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2
COEFFICIENTS
the coefficients of the arguments in your function
=-0.509,0.468,0.025,0.031,-0.211,-0.003,-0.008,0.239,-0.218,-0.002,-0.004,-0.227,-0.019,0.005,0.006,-0.006,-0.173,0.106,0.430,0.090,0.289,0.015,0.029
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO eig3:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2
COEFFICIENTS
the coefficients of the arguments in your function
=-0.367,0.354,-0.078,-0.003,0.104,-0.008,-0.118,0.424,-0.307,-0.011,0.063,0.077,-0.059,0.119,0.014,0.004,0.175,-0.558,0.237,0.089,0.013,0.021,0.022
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Multiple-walkers well-tempered metadynamics on the MC-HLDA eigenvectors
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
=metad
ARG
the input for this action is the scalar output from one or more other actions
=eig1,eig2
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=1.2
BIASFACTOR
use well tempered metadynamics and use this bias factor
=24
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15
SIGMA
the widths of the Gaussian hills
=0.015,0.015
FILE
a file in which the list of added hills is stored
=../HILLS
GRID_MIN
the lower bounds for the grid
=-0.1,-0.2
GRID_MAX
the upper bounds for the grid
=2.,2
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD
# Here we print all the data regarding metadynamics
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=metad
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
=metaD_data # Here we print all the data regarding barriers
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=d1.z,topwall.*,bottomwall
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 # Here we print all the data regarding ligand position and funnel 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
=d1.x,d1.y,d1.z,d1x,d1y,d1z,radius,funnel,funnelwall
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
=funnel_dist.dat # Here we print all the data regarding the MC-HLDA eigenvectors
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=eig1,eig2,eig3
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
=eigenvectors.dat # Here we print all the distances for the contacts
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=bound_d1,bound_d2,bound_d3,bound_d4,bound_d5,bound_d6,bound_d7,cl2_d1,cl2_d2,cl2_d3,cl2_d4,cl2_d5,cl2_d6,cl3_d1,cl3_d2,cl3_d3,cl3_d4,cl5_d1,cl5_d2,cl5_d3,cl5_d4,sb_d1,sb_d2
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
=contacts.dat
ENDPLUMED
Terminate plumed input. More details