PLUMED-NEST

Project ID: plumID:19.039
Source: plumed.dat
Originally used with PLUMED version: 2.6-dev
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

#RESTART

# To be used to force reconstruction of periodic boundary conditions
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=54,75,212,228,239,258,311,328,348,372,383,402,421,463,487,503,519,657,674,690,714,897,914,934,953,964,974,985,1007,1018,1037,1247,1264,1283,1302,1324,1689,1708,1727,1738,1962,1984,1994,2312,2329,2349,2467,2490,2500,2517,2524,2536,2547,2554,2569,2575,2591,2607,2635,2657,2676,2693,2700,2719,2735,2746,2770,2777,2788,2795,2805,2815,2832,2854,2868,2898,2904,2911,2927,2948,2962,2472,3221,3224,3225,3228,3229,3231,3233,3235,3237

The WHOLEMOLECULES action with label  calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2472,3224
ligThe COM action with label lig calculates the following quantities:
 Quantity   
 Type   
 Description  
lig
atoms
virtual atom calculated by COM action: 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

# This collective variable has the information of the position of the ligand with respect to the funnel-shape restraint potential. The reference file specified in REFERENCE should contain only the target molecule (no ligand, solvent, ecc.)
fpsThe FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Type   
 Description  
fps.lp
scalar
the position along the funnel line
fps.ld
scalar
the distance from the funnel line: 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

rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=start.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=start.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

# If not already present, FUNNEL will create the funnel potential and write it to the file specified in FILE
FUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. This action has hidden defaults. 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=BIAS LABELa label for the action so that its output can be referenced in the input to other actions=funnelThe FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Type   
 Description  
funnel.bias
scalar
the instantaneous value of the bias potential
FUNNELCalculate a funnel-shape restraint potential that is defined on a grid that is read during the setup. This action uses the defaults shown here. 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=BIAS LABELa label for the action so that its output can be referenced in the input to other actions=funnel  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0

# remove BIASFACTOR if you want to perform standard metadynamics
METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d1 SIGMAthe widths of the Gaussian hills=0.01 HEIGHTthe heights of the Gaussian hills=2.0 PACEthe frequency for hill addition=500 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=20 LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=4.0 GRID_WFILEthe file on which to write the grid=grid_w.dat GRID_WSTRIDEwrite the grid to a file every N steps=250000
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=d1 SIGMAthe widths of the Gaussian hills=0.01 HEIGHTthe heights of the Gaussian hills=2.0 PACEthe frequency for hill addition=500 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 BIASFACTORuse well tempered metadynamics and use this bias factor=20 LABELa label for the action so that its output can be referenced in the input to other actions=metad GRID_MINthe lower bounds for the grid=0.0 GRID_MAXthe upper bounds for the grid=4.0 GRID_WFILEthe file on which to write the grid=grid_w.dat GRID_WSTRIDEwrite the grid to a file every N steps=250000  FILE a file in which the list of added hills is stored=HILLS

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=-0.3 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=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.09 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=uwall-rmsdThe UPPER_WALLS action with label uwall-rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall-rmsd.bias
scalar
the instantaneous value of the bias potential
uwall-rmsd.force2
scalar
the instantaneous value of the squared force due to this bias potential
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=3.4 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=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=3.8 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=distwallThe UPPER_WALLS action with label distwall calculates the following quantities:
 Quantity   
 Type   
 Description  
distwall.bias
scalar
the instantaneous value of the bias potential
distwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

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