PLUMED-NEST

Click on the labels of the actions for more information on what each action computes

#RESTART
UNITSThis command sets the internal units for the code. More details ENERGYthe units of energy=kcal/mol LENGTHthe units of lengths=A

The UNITS action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=template.pdb
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=1-5761 ENTITY1the atoms that make up a molecule that you wish to align=5762-5825

p1: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=REPARAM_fnf.pdb  LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=6.06 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units=4 NEIGH_SIZEsize of the neighbor list=8

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####  CVs for free-energy reweighting  ####
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The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the pathc1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5816,5817,5819,5821,5823,5824
The COM action with label c1 calculates somethingc2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=5762,5763,5766,5768,5770,5772
The COM action with label c2 calculates somethingCV1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2
The DISTANCE action with label CV1 calculates the following quantities:
 Quantity   
 Description  
CV1.value
the DISTANCE between this pair of atomsCV2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c2,525

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####  Funnel definition  ####
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The DISTANCE action with label CV2 calculates the following quantities:
 Quantity   
 Description  
CV2.value
the DISTANCE between this pair of atomscom_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=5762,5763,5766,5768,5769,5770,5771,5772,5773,5774,5775,5780,5783,5786,5787,5788,5789,5792,5795,5798,5800,5801,5802,5803,5804,5806,5807,5808,5810,5811,5813,5815,5816,5817,5819,5821,5823,5824
The COM action with label com_lig calculates somethingfps: 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=com_lig REFERENCEa file in pdb format containing the structure you would like to align=funnel_ref.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=1785 POINTS6 values defining x, y, and z of the 2 points used to construct the line=77,1,16,90,5,28

The FUNNEL_PS action with label fps calculates the following quantities:
 Quantity   
 Description  
fps.lp
the position along the funnel line
fps.ld
the distance from the funnel lineFUNNELCalculate 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=32 ALPHAangle to change the width of the cone section=0.7 RCYLradius of the cylindrical section=1 MINSminimum value assumed by fps=2.5 MAXS maximum value assumed by fps=42 KAPPAconstant to be used for the funnel-shape restraint potential=1000 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

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####  Stepwise restraint over hinge-binder  ####
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The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the bias potentialrmsd_hb: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=rmsd_ref_ok.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

The RMSD action with label rmsd_hb calculates the following quantities:
 Quantity   
 Description  
rmsd_hb.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=rmsd_hb_restr
  ARGthe values input to this function=rmsd_hb,fps.lp
  VARthe names to give each of the arguments in the function=x,y
  FUNCthe function you wish to evaluate=x*(1-step(y-18))
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

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####  Stepwise restraint over hydrogen-bond counter  ####
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The MATHEVAL action with label rmsd_hb_restr calculates the following quantities:
 Quantity   
 Description  
rmsd_hb_restr.value
an arbitrary functiond1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1798,5788
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1783,5795
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1761,5792

The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomss1:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d1  FUNCthe function you wish to evaluate=0.5-1/pi*atan(9*(x-3)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label s1 calculates the following quantities:
 Quantity   
 Description  
s1.value
an arbitrary functions2:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d2  FUNCthe function you wish to evaluate=0.5-1/pi*atan(9*(x-3)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label s2 calculates the following quantities:
 Quantity   
 Description  
s2.value
an arbitrary functions3:  MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=d3  FUNCthe function you wish to evaluate=0.5-1/pi*atan(9*(x-3)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label s3 calculates the following quantities:
 Quantity   
 Description  
s3.value
an arbitrary functionhbc: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=s1,s2,s3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label hbc calculates the following quantities:
 Quantity   
 Description  
hbc.value
a linear combinationMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=hbc_restr
  ARGthe values input to this function=hbc,fps.lp
  VARthe names to give each of the arguments in the function=x,y
  FUNCthe function you wish to evaluate=x+1.5*step(y-18)
  PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

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####  Funnel-Metadynamics ####
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The MATHEVAL action with label hbc_restr calculates the following quantities:
 Quantity   
 Description  
hbc_restr.value
an arbitrary functionMETADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=meta
#RESTART=YES
ARGthe labels of the scalars on which the bias will act=fps.lp,p1.sss
SIGMAthe widths of the Gaussian hills=0.75,0.15 HEIGHTthe heights of the Gaussian hills=0.4 PACEthe frequency for hill addition=500
BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
GRID_MINthe lower bounds for the grid=0,-1 GRID_MAXthe upper bounds for the grid=42,14 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05,0.01
GRID_WFILEthe file on which to write the grid=grid.dat GRID_WSTRIDEwrite the grid to a file every N steps=50000
FILE a file in which the list of added hills is stored=HILLS
WALKERS_DIRshared directory with the hills files from all the walkers=../HILLS
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potential
meta.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
meta.rct
the reweighting factor c(t)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=10  KAPPAthe force constant for the wall=1000 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=lwall
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_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=40  KAPPAthe force constant for the wall=1000 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
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_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=8   KAPPAthe force constant for the wall=1000 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=ldwall
The UPPER_WALLS action with label ldwall calculates the following quantities:
 Quantity   
 Description  
ldwall.bias
the instantaneous value of the bias potential
ldwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details  ARGthe arguments on which the bias is acting=rmsd_hb_restr ATthe positions of the wall=4   KAPPAthe force constant for the wall=0.5  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=rmsdwall
The UPPER_WALLS action with label rmsdwall calculates the following quantities:
 Quantity   
 Description  
rmsdwall.bias
the instantaneous value of the bias potential
rmsdwall.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details  ARGthe arguments on which the bias is acting=hbc_restr     ATthe positions of the wall=1.5 KAPPAthe force constant for the wall=50   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=hbcwall

The LOWER_WALLS action with label hbcwall calculates the following quantities:
 Quantity   
 Description  
hbcwall.bias
the instantaneous value of the bias potential
hbcwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details   ARGthe labels of the values that you would like to print to the file=*  STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR

ENDPLUMEDTerminate plumed input. More details