Project ID: plumID:25.006
Source: Input_Files/plumed_pbmetad.dat
Originally used with PLUMED version: 2.8.2
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
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## This PLUMED input file should be used to run the PB-MetaD simulations ## It defines all the collective variables used in the biasing and analysis
## Energy and volume energy: ENERGYCalculate the total potential energy of the simulation box. More details volume: VOLUMECalculate the volume the simulation box. More details
## Defining the center atoms for each heavy moieties tbut: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=26-29 s_vhl: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=2-6 n_vhl: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=17-22 ph_brd4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=63-69 ph_vhl: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=7-12 S_5ring_brd4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=55-57,59,61 N_ring_brd4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=47-49,54,55,61,62 N_5ring_brd4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=49-52,54 linker: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=33-42 ## Defining distances between the brd4 and vhl moieties d_tbut_ph_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=tbut,ph_brd4 d_tbut_S_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=tbut,S_5ring_brd4 d_tbut_N_ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=tbut,N_ring_brd4 d_tbut_N_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=tbut,N_5ring_brd4 d_ph_brd4_linker: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_brd4,linker d_ph_vhl_linker: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_vhl,linker d_ph_brd4_ph_vhl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_brd4,ph_vhl d_ph_vhl_S_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_vhl,S_5ring_brd4 d_ph_vhl_N_ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_vhl,N_ring_brd4 d_ph_vhl_N_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_vhl,N_5ring_brd4 d_s_vhl_ph_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=s_vhl,ph_brd4 d_s_S_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=s_vhl,S_5ring_brd4 d_s_N_ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=s_vhl,N_ring_brd4 d_s_N_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=s_vhl,N_5ring_brd4 d_n_vhl_ph_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=n_vhl,ph_brd4 d_n_vhl_S_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=n_vhl,S_5ring_brd4 d_n_vhl_N_ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=n_vhl,N_ring_brd4 d_n_vhl_N_5ring_brd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=n_vhl,N_5ring_brd4 ## Calculating radius of gyration using the backbone C-atoms rgyr: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,2,4,6,7,8,9,10,11,12,13,15,17,18,19,21,23,25,26,27,28,29,31,33,35,36,38,39,41,42,44,46,47,49,52,53,55,57,58,59,60,61,62,63,64,65,66,67,68,69 ## Defining dihedral angles t_brd4_1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=50,49,47,46 t_brd4_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=69,63,62,48 t_brd4_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=63,62,48,47 t_brd4_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=48,47,46,44 t_brd4_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=47,46,44,43 t_brd4_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=46,44,43,42 t_brd4_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=44,43,42,41 t_linker_1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=43,42,41,40 t_linker_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=42,41,40,39 t_linker_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=41,40,39,38 t_linker_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=40,39,38,37 t_linker_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=39,38,37,36 t_linker_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=38,37,36,35 t_linker_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=37,36,35,34 t_linker_8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=36,35,34,33 t_linker_9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=35,34,33,31 t_vhl_1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=34,33,31,30 t_vhl_2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=33,31,30,25 t_vhl_3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,30,25,23 t_vhl_4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=30,25,23,22 t_vhl_5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,23,22,17 t_vhl_6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=23,22,17,15 t_vhl_7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=22,17,15,14 t_vhl_8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=17,15,14,13 t_vhl_9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,14,13,12 t_vhl_10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=14,13,12,9 t_vhl_11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=13,12,9,8 t_vhl_12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=8,7,6,2 t_vhl_13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,6,2,1 ## Bias parameters PBMETADUsed to performed Parallel Bias metadynamics. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=pbmetad ARGthe labels of the scalars on which the bias will act=t_brd4_4,t_brd4_5,t_brd4_6,t_brd4_7,t_linker_1,t_linker_2,t_linker_3,t_linker_4,t_linker_5,t_linker_6,t_linker_7,t_linker_8,t_linker_9,t_vhl_1,t_vhl_2,t_vhl_3,t_vhl_4,t_vhl_5,t_vhl_6,t_vhl_7,t_vhl_8,t_vhl_9,t_vhl_10,t_vhl_11,t_vhl_12,t_vhl_13 PACEthe frequency for hill addition, one for all biases=250 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=24 HEIGHTthe height of the Gaussian hills, one for all biases=0.3 SIGMAthe widths of the Gaussian hills=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2 GRID_MINthe lower bounds for the grid=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi GRID_MAXthe upper bounds for the grid=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi ... PBMETAD
## PACE value of 250 means that the bias will be updated every 250 steps. ## BIASFACTOR parameter controls the strength of the biasing potential applied to the selected collective variables (CVs). A higher bias factor generally leads to a stronger biasing force. ## HEIGHT parameter defines the height of the Gaussian biasing potential applied to the CVs. It determines how much bias is applied at the center of the Gaussian, with a higher value indicating a stronger bias. ## SIGMA parameter defines the width of the Gaussian biasing potential for each CV. In this case, it appears to be a list of values (0.2 for each CV) that specifies how spread out the Gaussian functions are for each of the selected atoms/groups. ## GRID_MIN sets the minimum values for the grid points in the multidimensional space defined by the CVs. The values are set to -pi for each CV, indicating the lower bound of the biasing potential. ## GRID_MAX sets the maximum values for the grid points in the multidimensional space defined by the CVs. The values are set to pi for each CV, indicating the upper bound of the biasing potential.
PRINTPrint quantities to a file. More details ... ARGthe labels of the values that you would like to print to the file=rgyr,energy,volume,pbmetad.* FILEthe name of the file on which to output these quantities=colvar_main.data STRIDE the frequency with which the quantities of interest should be output=500 ...
PRINTPrint quantities to a file. More details ... ARGthe labels of the values that you would like to print to the file=d_tbut_ph_brd4,d_tbut_S_5ring_brd4,d_tbut_N_ring_brd4,d_tbut_N_5ring_brd4,d_ph_brd4_linker,d_ph_vhl_linker,d_ph_brd4_ph_vhl,d_ph_vhl_S_5ring_brd4,d_ph_vhl_N_ring_brd4,d_ph_vhl_N_5ring_brd4,d_s_vhl_ph_brd4,d_s_S_5ring_brd4,d_s_N_ring_brd4,d_s_N_5ring_brd4,d_n_vhl_ph_brd4,d_n_vhl_S_5ring_brd4,d_n_vhl_N_ring_brd4,d_n_vhl_N_5ring_brd4,pbmetad.* FILEthe name of the file on which to output these quantities=colvar_distances.data STRIDE the frequency with which the quantities of interest should be output=500 ...
PRINTPrint quantities to a file. More details ... ARGthe labels of the values that you would like to print to the file=t_brd4_1,t_brd4_2,t_brd4_3,t_brd4_4,t_brd4_5,t_brd4_6,t_brd4_7,t_linker_1,t_linker_2,t_linker_3,t_linker_4,t_linker_5,t_linker_6,t_linker_7,t_linker_8,t_linker_9,t_vhl_1,t_vhl_2,t_vhl_3,t_vhl_4,t_vhl_5,t_vhl_6,t_vhl_7,t_vhl_8,t_vhl_9,t_vhl_10,t_vhl_11,t_vhl_12,t_vhl_13,pbmetad.* FILEthe name of the file on which to output these quantities=colvar_angles.data STRIDE the frequency with which the quantities of interest should be output=500 ...