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| This is part of the funnel module | |
| It is only available if you configure PLUMED with ./configure –enable-modules=funnel . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
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.
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.
lig: COMATOMS=3221,3224,3225,3228,3229,3231,3233,3235,3237 fps: FUNNEL_PSthe list of atoms which are involved the virtual atom's definition.LIGAND=ligThis MUST be a single atom, normally the COM of the ligand.REFERENCE=start.pdbcompulsory keyword a file in pdb format containing the structure you would like to align.ANCHOR=2472Closest protein atom to the ligand, picked to avoid pbc problems during the simulation.POINTS=4.724,5.369,4.069,4.597,5.721,4.343 funnel: FUNNELcompulsory keyword 6 values defining x, y, and z of the 2 points used to construct the line.ARG=fps.lp,fps.ldcompulsory keyword the labels of the scalars on which the bias will actZCC=1.8compulsory keyword ( default=ZCC ) switching point between cylinder and coneALPHA=0.55angle to change the width of the cone sectionRCYL=0.1radius of the cylindrical sectionMINS=-0.5minimum value assumed by fps.lp,MAXS=3.7compulsory keyword ( default=MAXS ) maximum value assumed by fps.lpKAPPA=35100constant to be used for the funnel-shape restraint potentialNBINS=500number of bins along fps.lpNBINZ=500number of bins along fps.ldFILE=BIAScompulsory keyword name of the Funnel potential file
The BIAS will then look something like this:
#! 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 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.
lig: COMATOMS=545,546,547,548,549,550,551,552,553 fps: FUNNEL_PSthe list of atoms which are involved the virtual atom's definition.LIGAND=ligThis MUST be a single atom, normally the COM of the ligand.REFERENCE=ref.pdbcompulsory keyword a file in pdb format containing the structure you would like to align.ANCHOR=52Closest protein atom to the ligand, picked to avoid pbc problems during the simulation.POINTS=2.793,3.696,3.942,3.607,4.298,3.452 funnel: FUNNELcompulsory keyword 6 values defining x, y, and z of the 2 points used to construct the line.ARG=fps.lp,fps.ldcompulsory keyword the labels of the scalars on which the bias will actZCC=4.0compulsory keyword ( default=ZCC ) switching point between cylinder and coneRCYL=0.1radius of the cylindrical sectionMINS=0.2minimum value assumed by fps.lp,MAXS=4.9compulsory keyword ( default=MAXS ) maximum value assumed by fps.lpKAPPA=100000constant to be used for the funnel-shape restraint potentialNBINS=500number of bins along fps.lpNBINZ=500number of bins along fps.ldSPHERE( default=off ) The Funnel potential including the binding site can be spherical instead of a coneSAFETY=1.0To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)FILE=BIAScompulsory keyword name of the Funnel potential file
By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
| Quantity | Description |
| bias | the instantaneous value of the bias potential |
| ARG | the labels of the scalars on which the bias will act |
| SCALE | ( default=1.0 ) a factor that multiplies the external potential, useful to invert free energies |
| MAXS | ( default=MAXS ) maximum value assumed by fps.lp |
| ZCC | ( default=ZCC ) switching point between cylinder and cone |
| FILE | name of the Funnel potential file |
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOSPLINE | ( default=off ) specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential |
| SPARSE | ( default=off ) specifies that the external potential uses a sparse grid |
| SPHERE | ( default=off ) The Funnel potential including the binding site can be spherical instead of a cone |
| WALKERS_MPI | ( default=off ) To be used when gromacs + multiple walkers are used |
| NBINS | number of bins along fps.lp |
| NBINZ | number of bins along fps.ld |
| MINS | minimum value assumed by fps.lp, if the ligand is able to go beyond this value the simulation will crash |
| KAPPA | constant to be used for the funnel-shape restraint potential |
| RCYL | radius of the cylindrical section |
| SAFETY | To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm) |
| SLOPE | Adjust the behavior of the potential outside the funnel, greater values than 1.0 will tend to push the ligand more towards the cylinder and vice versa |
| ALPHA | angle to change the width of the cone section |
1.8.17