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Action: FUNNEL_PS

Module funnel
Description Usage
FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. used in 0 tutorialsused in 5 eggs

Details and examples

FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2.

Please read the first two papers in the references below to better understand the notions hereby reported.

This colvar evaluates the position of a ligand of interest with respect to a given line, built from the two points A and B, and should be used together with the FUNNEL bias. The constructed line represents the axis of the funnel-shape restraint potential, which should be placed so as to include the portion of a macromolecule (i.e., protein, DNA, etc.) that should be explored. Since it is important that the position of the line is updated based on the motion of the macromolecule during the simulation, this colvar incorporates an alignment method. The latter uses the TYPE=OPTIMAL option to remove motions due to rotation and translation of the macromolecule with respect to a reference structure, which is provided by the user. In order to accomplish the task, an optimal alignment matrix is calculated using the Kearsley algorithm that is discussed in the third paper cited below. The reference structure should be given as a pdb file, containing only the atoms of the macromolecule or a selection of them (e.g., the protein CA atoms of secondary structures). In contrast to the methods discussed in the documentation for RMSD, the values reported in the occupancy and beta-factor columns of the pdb file are not important since they will be overwritten and replaced by the value 1.00 during the procedure. It is important to understand that all atoms in the file will be used for the alignment, even if they display 0.00 in the occupancy column.

The ligand can be represented by one single atom or the center of mass (COM) of a group of atoms that should be provided by the user.

By default FUNNEL_PS is computed taking into account periodic boundary conditions. Since PLUMED 2.5, molecules are rebuilt using a procedure that is equivalent to that done in WHOLEMOLECULES. We note that this action is local to this colvar, thus it does not modify the coordinates stored in PLUMED. Moreover, FUNNEL_PS requires an ANCHOR atom to be specified in order to facilitate the reconstruction of periodic boundary conditions. This atom should be the closest macromolecule's atom to the ligand and it should reduce the risk of ligand "warping" in the simulation box. Nevertheless, we highly recommend to add to the PLUMED input file a custom line of WHOLEMOLECULES, in order to be sure of reconstructing the ligand together with the macromolecule (please look the examples). In this case, the user can use the NOPBC flag to turn off the internal periodic boundary condition reconstruction.

FUNNEL_PS is divided in two components (fps.lp and fps.ld) which evaluate the projection of the ligand along the funnel line and the distance from it, respectively. The values attributed to these two components are then used together with the potential file created by the FUNNEL bias to define if the ligand is within or not in the funnel-shape restraint potential. In the latter case, the potential will force the ligand to enter within the funnel boundaries.

Examples

The following input tells plumed to print the FUNNEL_PS components for the COM of a ligand. The inputs are a reference structure, which is the structure used for the alignment, the COM of the molecule we want to track, and 2 points in the Cartesian space (i.e., x, y, and z) to draw the line representing the funnel axis.

Click on the labels of the actions for more information on what each action computes
tested on2.11
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=2446,2447,2448,2449,2451
fps: FUNNEL_PSFUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2. More details REFERENCEa file in pdb format containing the structure you would like to align=protein.pdb LIGANDThis MUST be a single atom, normally the COM of the ligand=lig POINTS6 values defining x, y, and z of the 2 points used to construct the line=5.3478,-0.7278,2.4746,7.3785,6.7364,-9.3624
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=fps.lp,fps.ld

It is recommended to add a line to force the reconstruction of the periodic boundary conditions. In the following example, WHOLEMOLECULES was added to make sure that the ligand was reconstructed together with the protein. The list contains all the atoms reported in the start.pdb file followed by the ANCHOR atom and the ligand. All atoms should be contained in the same entity and the correct order.

Click on the labels of the actions for more information on what each action computes
tested on2.11
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=54,75,212,228,239,258,311,328,348,372,383,402,421,463,487,503,519,657,674,690,714,897,914,934,953,964,
974This action is not part of PLUMED and was included by using a LOAD command More details985100710181037124712641283130213241689170817271738196219841994231223292349246724902500251725242536
2547This action is not part of PLUMED and was included by using a LOAD command More details255425692575259126072635265726762693270027192735274627702777278827952805281528322854286828982904
2911This action is not part of PLUMED and was included by using a LOAD command More details2927294829622472322132243225322832293231323332353237
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
fps: 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=fps.lp,fps.ld

Input

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

Keyword Type Description
LIGAND atoms This MUST be a single atom, normally the COM of the ligand
ANCHOR atoms Closest protein atom to the ligand, picked to avoid pbc problems during the simulation

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Description
lp scalar the position along the funnel line
ld scalar the distance from the funnel line

Full list of keywords

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

Keyword Type Default Description
LIGAND input none This MUST be a single atom, normally the COM of the ligand
ANCHOR input none Closest protein atom to the ligand, picked to avoid pbc problems during the simulation
REFERENCE compulsory none a file in pdb format containing the structure you would like to align
POINTS compulsory none 6 values defining x, y, and z of the 2 points used to construct the line
NUMERICAL_DERIVATIVESThis keyword do not have examples optional false calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples optional false ignore the periodic boundary conditions when calculating distances
SQUARED-ROOTThis keyword do not have examples optional false Used to initialize the creation of the alignment variable

References

More information about how this action can be used is available in the following articles: