PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:21.012
Source: plumed-nest/wild/plumed.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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

# COLVAR
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=5533-5577 # you need the COM of your ligand/molecule
pbd1The COM action with label pbd1 calculates the following quantities: Quantity    Type    Description  
pbd1 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=3261-3284 # describe product binding domain (res 213)
pbd2The COM action with label pbd2 calculates the following quantities: Quantity    Type    Description  
pbd2 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=3736-3756 # describe prroduct binding domain (res 245)
wallresThe COM action with label wallres calculates the following quantities: Quantity    Type    Description  
wallres 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=4335-4349 # lower wall on deep active site residue

# FUNNEL
wdThe DISTANCE action with label wd calculates the following quantities: Quantity    Type    Description  
wd 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=3616,lig # anchor dist for walls 
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 REFERENCEa file in pdb format containing the structure you would like to align=ref.pdb LIGANDThis MUST be a single atom, normally the COM of the ligand=lig ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=3616 POINTS6 values defining x, y, and z of the 2 points used to construct the line=5.1375,4.3952,5.3672,6.5414,3.6569,5.4359

d1The 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=pbd1,lig # For the meta, not Funnel related
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 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=pbd2,lig
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 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=wallres,lig

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=2.5 ALPHAangle to change the width of the cone section=0.55 RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=-1 MAXS maximum value assumed by fps=6 KAPPAconstant to be used for the funnel-shape restraint potential=50000 NBINSnumber of bins along fps=500 NBINZnumber of bins along fps=500 SAFETYTo be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)=1.0 SLOPEAdjust the behavior of the potential outside the funnel, greater values than 1=1.0 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 FILEname of the Funnel potential file=BIAS
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=2.5 ALPHAangle to change the width of the cone section=0.55 RCYLradius of the cylindrical section=0.1 MINSminimum value assumed by fps=-1 MAXS maximum value assumed by fps=6 KAPPAconstant to be used for the funnel-shape restraint potential=50000 NBINSnumber of bins along fps=500 NBINZnumber of bins along fps=500 SAFETYTo be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)=1.0 SLOPEAdjust the behavior of the potential outside the funnel, greater values than 1=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnel FILEname of the Funnel potential file=BIAS  SCALE a factor that multiplies the external potential, useful to invert free energies=1.0

### 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,fps.lp
    SIGMAthe widths of the Gaussian hills=0.05,0.05
    HEIGHTthe heights of the Gaussian hills=2.5 #kj/mol
    PACEthe frequency for hill addition=1000
    BIASFACTORuse well tempered metadynamics and use this bias factor=8
    TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
    GRID_MINthe lower bounds for the grid=-0.5,-1
    GRID_MAXthe upper bounds for the grid=5.0,6.0
    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 # Not Funnel related
... METAD
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,fps.lp
    SIGMAthe widths of the Gaussian hills=0.05,0.05
    HEIGHTthe heights of the Gaussian hills=2.5 #kj/mol
    PACEthe frequency for hill addition=1000
    BIASFACTORuse well tempered metadynamics and use this bias factor=8
    TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
    GRID_MINthe lower bounds for the grid=-0.5,-1
    GRID_MAXthe upper bounds for the grid=5.0,6.0
    LABELa label for the action so that its output can be referenced in the input to other actions=metad # Not Funnel related
 FILE a file in which the list of added hills is stored=HILLS
... METAD

### WALLS ###
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=4.0 KAPPAthe force constant for the wall=500000.0 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=uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities: Quantity    Type    Description  
uwall1.bias scalar the instantaneous value of the bias potential
uwall1.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.ld ATthe positions of the wall=1.0 KAPPAthe force constant for the wall=500000.0 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=uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities: Quantity    Type    Description  
uwall2.bias scalar the instantaneous value of the bias potential
uwall2.force2 scalar the instantaneous value of the squared force due to this bias potential

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=0.00 KAPPAthe force constant for the wall=500000.0 EXP the powers for the walls=3 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=lwall1The LOWER_WALLS action with label lwall1 calculates the following quantities: Quantity    Type    Description  
lwall1.bias scalar the instantaneous value of the bias potential
lwall1.force2 scalar the instantaneous value of the squared force due to this bias potential
LOWER_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=0.0 KAPPAthe force constant for the wall=500000.0 EXP the powers for the walls=3 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=lwall2The LOWER_WALLS action with label lwall2 calculates the following quantities: Quantity    Type    Description  
lwall2.bias scalar the instantaneous value of the bias potential
lwall2.force2 scalar the instantaneous value of the squared force due to this bias potential
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3 ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=500000.0 LABELa label for the action so that its output can be referenced in the input to other actions=reswallThe LOWER_WALLS action with label reswall calculates the following quantities: Quantity    Type    Description  
reswall.bias scalar the instantaneous value of the bias potential
reswall.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=1000 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
Quantity	Type	Description
lig	atoms	virtual atom calculated by COM action
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
