PLUMED-NEST

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

#
# 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
COMCalculate the center of mass for a group of atoms. More details ATOMSthe 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  LABELa 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
COMCalculate the center of mass for a group of atoms. More details ATOMSthe 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 LABELa 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)
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ixo,pkt LABELa 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: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1.x PERIODICif 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: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1.y PERIODICif 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: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1.z PERIODICif 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) 
radiusThe MATHEVAL action with label radius calculates the following quantities:
 Quantity   
 Type   
 Description  
radius
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d1x,d1y VARthe names to give each of the arguments in the function=x,y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif 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
funnelThe MATHEVAL action with label funnel calculates the following quantities:
 Quantity   
 Type   
 Description  
funnel
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=radius,d1z VARthe names to give each of the arguments in the function=r,z FUNCthe function you wish to evaluate=(r-(z+1.8))*step(z+1.7)+(r-0.1)*step(-1.7-z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# We define the funnel potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0 ARGthe arguments on which the bias is acting=funnel KAPPAthe force constant for the wall=2000.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnelwallThe UPPER_WALLS action with label funnelwall calculates the following quantities:
 Quantity   
 Type   
 Description  
funnelwall.bias
scalar
the instantaneous value of the bias potential
funnelwall.force2
scalar
the instantaneous value of the squared force due to this bias potential


# Wall on distance to prevent the ligand exit to the solvent
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=-4.0 ARGthe arguments on which the bias is acting=d1.z KAPPAthe force constant for the wall=2000.0 LABELa label for the action so that its output can be referenced in the input to other actions=topwallThe LOWER_WALLS action with label topwall calculates the following quantities:
 Quantity   
 Type   
 Description  
topwall.bias
scalar
the instantaneous value of the bias potential
topwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
# Wall on distance to prevent the ligand entering the intracellular part
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0.3 ARGthe arguments on which the bias is acting=d1.z KAPPAthe force constant for the wall=2000.0 LABELa label for the action so that its output can be referenced in the input to other actions=bottomwallThe UPPER_WALLS action with label bottomwall calculates the following quantities:
 Quantity   
 Type   
 Description  
bottomwall.bias
scalar
the instantaneous value of the bias potential
bottomwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

# Contact related to the nonbonded interactions in bound state
bound_d1The DISTANCE action with label bound_d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,3637
bound_d2The DISTANCE action with label bound_d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,3637
bound_d3The DISTANCE action with label bound_d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,2842
bound_d4The DISTANCE action with label bound_d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,2837
bound_d5The DISTANCE action with label bound_d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,3620
bound_d6The DISTANCE action with label bound_d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,1505
bound_d7The DISTANCE action with label bound_d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
bound_d7
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,1398

# Contact related to the nonbonded interactions in state A 
cl2_d1The DISTANCE action with label cl2_d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,1409
cl2_d2The DISTANCE action with label cl2_d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,1409
cl2_d3The DISTANCE action with label cl2_d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,1456
cl2_d4The DISTANCE action with label cl2_d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,1411
cl2_d5The DISTANCE action with label cl2_d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d5
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=19,3622
cl2_d6The DISTANCE action with label cl2_d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl2_d6
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,1408

# Contact related to the nonbonded interactions in state B
cl3_d1The DISTANCE action with label cl3_d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl3_d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,1404
cl3_d2The DISTANCE action with label cl3_d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl3_d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,3975
cl3_d3The DISTANCE action with label cl3_d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl3_d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,1413
cl3_d4The DISTANCE action with label cl3_d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl3_d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,3613

# Contact related to the nonbonded interactions in state C
cl5_d1The DISTANCE action with label cl5_d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl5_d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,3618
cl5_d2The DISTANCE action with label cl5_d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl5_d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,3618
cl5_d3The DISTANCE action with label cl5_d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl5_d3
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=23,3615
cl5_d4The DISTANCE action with label cl5_d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cl5_d4
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=29,2791

# Salt bridges
sb_d1The DISTANCE action with label sb_d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
sb_d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,1392
sb_d2The DISTANCE action with label sb_d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
sb_d2
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,1393

# Eigenvectors from the MC-HLDA analysis on the contacts
eig1The COMBINE action with label eig1 calculates the following quantities:
 Quantity   
 Type   
 Description  
eig1
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
eig2The COMBINE action with label eig2 calculates the following quantities:
 Quantity   
 Type   
 Description  
eig2
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
eig3The COMBINE action with label eig3 calculates the following quantities:
 Quantity   
 Type   
 Description  
eig3
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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 PERIODICif 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
METADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
ARGthe labels of the scalars on which the bias will act=eig1,eig2
PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.2 
BIASFACTORuse well tempered metadynamics and use this bias factor=24.
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.15
SIGMAthe widths of the Gaussian hills=0.015,0.015
FILE a file in which the list of added hills is stored=../HILLS 
GRID_MINthe lower bounds for the grid=-0.1,-0.2
GRID_MAXthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=metad.* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=metaD_data
# Here we print all the data regarding barriers
The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1.z,topwall.*,bottomwall.* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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 FILEthe name of the file on which to output these quantities=funnel_dist.dat
# Here we print all the data regarding the MC-HLDA eigenvectors 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=eig1,eig2,eig3 STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=eigenvectors.dat
# Here we print all the distances for the contacts 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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 FILEthe name of the file on which to output these quantities=contacts.dat

ENDPLUMEDTerminate plumed input. More details