Action: FUNNEL

Module	funnel
Description	Usage
Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup.

Details and examples

Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup.

If the input file is not already present, it will create one with the name specified in the FILE flag. The potential has a two-dimensional resolution since it has been devised to be used with the two components of FUNNEL_PS (i.e., fps.lp and fps.ld) and it is divided in two sections, a cone shape attached to a cylindrical one. The user can customize the shape of both the sections by modifying a number of flags. In particular the cone section of the funnel is calculated with the following formula:

$$MAX_Z=R_{cyl} + tg_{alpha} * (z_{cc} - MIN_S)$$

where $MAX_Z$ is the radius of the cone base, $R_{cyl}$ is the radius of the cylinder part, $tg_{alpha}$ is the angle regulating how steep the cone is, $z_{cc}$ is the switching point between cone and cylinder, and $MIN_S$ is the lowest possible value assumed by fps.lp of FUNNEL_PS. As for the cylinder, it starts from the value of $z_{cc}$ and stops at the value of $MAX_S$ with a section of $pi*r_{cyl}^2$.

There is the option of transforming the cone region into a sphere with the use of the SPHERE flag. In this case, the new shape will have a radius of $z_{cc}$. It might be necessary tuning the SAFETY option to select how much the potential extends from the sphere.

Examples

The following is an input for a calculation with a funnel potential that is defined in the file BIAS and that acts on the collective variables defined by FUNNEL_PS.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/funnel/rt-funnel/BIAS.reference INPUTFILELINES=1-15

lig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3221,3224,3225,3228,3229,3231,3233,3235,3237
The COM action with label lig calculates somethingfps: FUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details LIGANDThis MUST be a single atom, normally the COM of the ligand=lig REFERENCEa file in pdb format containing the structure you would like to align=start.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=2472 POINTS6 values defining x, y, and z of the 2 points used to construct the line=4.724,5.369,4.069,4.597,5.721,4.343

The FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Description  
fps.lp
the position along the funnel line
fps.ld
the distance from the funnel linefunnel: FUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. More details ...
   ARGthe labels of the scalars on which the bias will act=fps.lp,fps.ld ZCC switching point between cylinder and cone=1.8 ALPHAangle to change the width of the cone section=0.55
   RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=-0.5 MAXS maximum value assumed by fps=3.7 KAPPAconstant to be used for the funnel-shape restraint potential=35100
   NBINSnumber of bins along fps=500 NBINZnumber of bins along fps=500
   FILEname of the Funnel potential file=
regtest/funnel/rt-funnel/BIAS.reference
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/funnel/rt-funnel/BIAS.reference
    
#! FIELDS fps.lp fps.ld funnel.bias der_fps.lp der_fps.ld 
#! SET min_fps.lp -0.500000
#! SET max_fps.lp 3.700000
#! SET nbins_fps.lp 500.000000
#! SET periodic_fps.lp false
#! SET min_fps.ld 0.000000
#! SET max_fps.ld 1.510142
#! SET nbins_fps.ld 500.000000
#! SET periodic_fps.ld false
    -0.500000      0.000000      0.000000      0.000000      0.000000
    -0.500000      0.003020      0.000000      0.000000      0.000000
    -0.500000      0.006041      0.000000      0.000000      0.000000
    -0.500000      0.009061      0.000000      0.000000      0.000000
    -0.500000      0.012081      0.000000      0.000000      0.000000
    -0.500000      0.015101      0.000000      0.000000      0.000000
  
...
The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the bias potential

The Funnel potential should always be used in combination with the collective variable FUNNEL_PS, since it is constructed to take as inputs fps.lp and fps.ld (the former linepos and linedist of Funnel-Metadynamics FM). In the first block of data the value of fps.lp (the value in the first column) is kept fixed and the value of the function is given at 500 equally spaced values for fps.ld between 0 and 1.51. In the second block of data fps.lp is fixed at $-0.5 + \frac{4.2}{500}$ and the value of the function is given at 500 equally spaced values for fps.ld between 0 and 1.51. In the third block of data the same is done but fps.lp is fixed at $-0.5 + \frac{8.4}{100}$ and so on until you get to the five hundredth block of data where fps.lp is fixed at $3.7$.

It is possible to switch the shape of the cone region, transforming it in a sphere, with the flag SPHERE.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/funnel/rt-funnel/BIAS.reference INPUTFILELINES=1-15

lig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=545,546,547,548,549,550,551,552,553
The COM action with label lig calculates somethingfps: FUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details LIGANDThis MUST be a single atom, normally the COM of the ligand=lig REFERENCEa file in pdb format containing the structure you would like to align=ref.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=52 POINTS6 values defining x, y, and z of the 2 points used to construct the line=2.793,3.696,3.942,3.607,4.298,3.452

The FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Description  
fps.lp
the position along the funnel line
fps.ld
the distance from the funnel linefunnel: FUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. More details ...
   ARGthe labels of the scalars on which the bias will act=fps.lp,fps.ld ZCC switching point between cylinder and cone=4.0 RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=0.2
   MAXS maximum value assumed by fps=4.9 KAPPAconstant to be used for the funnel-shape restraint potential=100000 NBINSnumber of bins along fps=500
   NBINZnumber of bins along fps=500 SPHERE The Funnel potential including the binding site can be spherical instead of a cone SAFETYTo be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)=1.0
   FILEname of the Funnel potential file=
regtest/funnel/rt-funnel/BIAS.reference
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/funnel/rt-funnel/BIAS.reference
    
#! FIELDS fps.lp fps.ld funnel.bias der_fps.lp der_fps.ld 
#! SET min_fps.lp -0.500000
#! SET max_fps.lp 3.700000
#! SET nbins_fps.lp 500.000000
#! SET periodic_fps.lp false
#! SET min_fps.ld 0.000000
#! SET max_fps.ld 1.510142
#! SET nbins_fps.ld 500.000000
#! SET periodic_fps.ld false
    -0.500000      0.000000      0.000000      0.000000      0.000000
    -0.500000      0.003020      0.000000      0.000000      0.000000
    -0.500000      0.006041      0.000000      0.000000      0.000000
    -0.500000      0.009061      0.000000      0.000000      0.000000
    -0.500000      0.012081      0.000000      0.000000      0.000000
    -0.500000      0.015101      0.000000      0.000000      0.000000
  
...
The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the bias potential

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the scalars on which the bias will act

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the labels of the scalars on which the bias will act
SCALEThis keyword do not have examples	compulsory	1.0	a factor that multiplies the external potential, useful to invert free energies
MAXS	compulsory	MAXS	maximum value assumed by fps
ZCC	compulsory	ZCC	switching point between cylinder and cone
FILE	compulsory	none	name of the Funnel potential file
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOSPLINEThis keyword do not have examples	optional	false	specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential
SPARSEThis keyword do not have examples	optional	false	specifies that the external potential uses a sparse grid
SPHERE	optional	false	The Funnel potential including the binding site can be spherical instead of a cone
NBINS	optional	not used	number of bins along fps
NBINZ	optional	not used	number of bins along fps
MINS	optional	not used	minimum value assumed by fps
KAPPA	optional	not used	constant to be used for the funnel-shape restraint potential
RCYL	optional	not used	radius of the cylindrical section
SAFETY	optional	not used	To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)
SLOPEThis keyword do not have examples	optional	not used	Adjust the behavior of the potential outside the funnel, greater values than 1
ALPHA	optional	not used	angle to change the width of the cone section
WALKERS_MPIThis keyword do not have examples	optional	false	To be used when gromacs + multiple walkers are used