Project ID: plumID:25.026
Source: Wildtype_inputs/plumed_F1.dat
Originally used with PLUMED version: 2.7
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
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=17561,17565,17568,17569,17570 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=6pm5_reft2.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=12947 POINTS6 values defining x, y, and z of the 2 points used to construct the line=5.3012,3.63,5.8176,5.5748,2.7964,5.8176 NOPBC ignore the periodic boundary conditions when calculating distances
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=2.5 ALPHAangle to change the width of the cone section=0.45 RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=-0.6 MAXS maximum value assumed by fps=3.6 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=BIAS LABELa label for the action so that its output can be referenced in the input to other actions=funnel
# remove BIASFACTOR if you want to perform standard metadynamics METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=fps.lp,fps.ld SIGMAthe widths of the Gaussian hills=0.02,0.02 HEIGHTthe heights of the Gaussian hills=1.2 PACEthe frequency for hill addition=500 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 BIASFACTORuse well tempered metadynamics and use this bias factor=15 GRID_MINthe lower bounds for the grid=-0.7,0 GRID_MAXthe upper bounds for the grid=3.7,1.6 GRID_WFILEthe file on which to write the grid=grid_1.dat GRID_WSTRIDEwrite the grid to a file every N steps=250000 LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=-0.5 KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=lp_lwall UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.lp ATthe positions of the wall=3.5 KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=lp_uwall UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=fps.ld ATthe positions of the wall=1.3 KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=ld_uwall
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR_1