PLUMED-NEST-TEST-SITE

Project ID: plumID:19.046
Source: PLUMED_FM/plumed_FM.dat
Originally used with PLUMED version: 2.5-mod
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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=protein.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-3232

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=3233,3236,3237,3240,3241,3243,3245,3247,3249 # you need the COM of your ligand/molecule

The COM action with label lig calculates somethingfps: FPSThis action is not part of PLUMED and was included by using a LOAD command More details REFERENCE=Faidon_new_ref.pdb LIGAND=lig ANCHOR=2481 POINTS=-0.5910,0.3486,-1.6694,-0.6214,0.5475,-1.2516
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# This is the colvar that has inside linepos and linedist (fps.lp and fps.ld, respectively).
# Starting form the obvious, POINTS are the two points A and B to construct the funnel,
# REFERENCE is a pdb file to align the target protein with the frame used to construct
# the funnel. LIGAND must have the label of the COM of the ligand. ANCHOR is one of the
# closest atoms of the protein with respect to the ligand. It's necessary to avoid pbc
# problems.
##############################################################################################

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 MINSminimum value assumed by fps=-1.0 MAXS maximum value assumed by fps=3.5 NBINSnumber of bins along fps=600 ZCC switching point between cylinder and cone=1.8 ALPHAangle to change the width of the cone section=0.55 KAPPAconstant to be used for the funnel-shape restraint potential=35100 LABELa label for the action so that its output can be referenced in the input to other actions=funnel
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# This routine creates the external BIAS of the Funnel. ARG is already set and should
# not be changed. S is the direction along linepos and MINS and MAXS define the maximum
# values that fps.lp can take. ATTENTION: if fps.lp takes a value outside this interval
# during the simulation, the simulation will crash. NBINS and NBINZ (not used here) 
# determine the binning of the external BIAS. ZCC and ALPHA regulate the shape and
# position of cone and cylinder. KAPPA is the constant used to evaluate the potential
# in each bin.
############################################################################################## 

#METAD ARG=d1 SIGMA=0.01 HEIGHT=2.0 PACE=500 BIASFACTOR=12 TEMP=300 LABEL=metad # Not Funnel related

The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the 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=3.0 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=uwall
##############################################################################################
# Here pick a value lower than MAXS, the ligand MUST NOT exit the grid
##############################################################################################

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 potentialLOWER_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=500000.0 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=lwall
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# Here pick a value greater than MINS, the ligand MUST NOT exit the grid
##############################################################################################
#This is the rmsd from the bound pose. It involves the atoms at play in the bound pose
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 potentialRMSDCalculate 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=pocket.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL LABELa label for the action so that its output can be referenced in the input to other actions=rmsd  
The RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputUPPER_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=1.2 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=rmsdwall # Not Funnel related, I am not allowing the ligand to fly to the solvent

#This rmsd restricts the CA momevement of the entire protein
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 potentialrmsdINIT: 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=my_start_meta.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsdINIT calculates the following quantities:
 Quantity   
 Description  
rmsdINIT.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsdINIT ATthe positions of the wall=0.09 KAPPAthe force constant for the wall=420000 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=rmsdwallINIT 

#####DESCRIPTORS#####
The UPPER_WALLS action with label rmsdwallINIT calculates the following quantities:
 Quantity   
 Description  
rmsdwallINIT.bias
the instantaneous value of the bias potential
rmsdwallINIT.force2
the instantaneous value of the squared force due to this bias potentialOW: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3251-47362:3
The GROUP action with label OW calculates somethingc1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2473-2495,2913-2919
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=3240
The COM action with label c2 calculates somethingdcm: 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 dcm calculates the following quantities:
 Quantity   
 Description  
dcm.value
the DISTANCE between this pair of atomsc3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2480
The COM action with label c3 calculates somethingc4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3236
The COM action with label c4 calculates somethingdsb: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c3,c4
The DISTANCE action with label dsb calculates the following quantities:
 Quantity   
 Description  
dsb.value
the DISTANCE between this pair of atomst: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2915,2780,3241,3247
The TORSION action with label t calculates the following quantities:
 Quantity   
 Description  
t.value
the TORSION involving these atomsw: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2481,2482,2492,2949 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=OW  LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4 NN=6 MM=12 D_MAX=0.5}
The DISTANCES action with label w calculates the following quantities:
 Quantity   
 Description  
w.lessthan
the number of colvars that have a value less than a threshold
w.value
the DISTANCES between the each pair of atoms that were specifiedBRIDGECalculate a matrix with elements equal to one if there is a bridging atom between the two atoms More details BRIDGING_ATOMSThe list of atoms that can form the bridge between the two interesting parts of the structure=OW GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=2805 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=2489 SWITCHThe parameters of the two switching functions in the above formula. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.6 D_0=0.0 NN=6 MM=10 D_MAX=4.0} LABELa label for the action so that its output can be referenced in the input to other actions=wBpock
The BRIDGE action with label wBpock calculates the following quantities:
 Quantity   
 Description  
wBpock.value
the number of bridging atoms between the two groupslig_OW_large: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3233,3236,3237,3240,3241,3243,3245,3247,3249 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=OW  LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.8 NN=6 MM=12 D_MAX=0.4}

##NORMALIZE DESCRITOPRS##
The DISTANCES action with label lig_OW_large calculates the following quantities:
 Quantity   
 Description  
lig_OW_large.lessthan
the number of colvars that have a value less than a threshold
lig_OW_large.value
the DISTANCES between the each pair of atoms that were specifiedCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=wBpock COEFFICIENTS the coefficients of the arguments in your function=0.1538 POWERS the powers to which you are raising each of the arguments in your function=1 LABELa label for the action so that its output can be referenced in the input to other actions=wBpock_norm PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label wBpock_norm calculates the following quantities:
 Quantity   
 Description  
wBpock_norm.value
a linear compbinationALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=2915,2780,3241,3247 REFERENCEthe reference values for each of the torsional angles=1.66
LABELa label for the action so that its output can be referenced in the input to other actions=ab_t
... ALPHABETA
The ALPHABETA action with label ab_t calculates the following quantities:
 Quantity   
 Description  
ab_t.value
the alpha beta CVProt:  DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3233,3236,3237,3240,3241,3243,3245,3247,3249 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-3232 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.32 NN=6 MM=12}
The DISTANCES action with label Prot calculates the following quantities:
 Quantity   
 Description  
Prot.lessthan
the number of colvars that have a value less than a threshold
Prot.value
the DISTANCES between the each pair of atoms that were specifiedCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=Prot.lessthan COEFFICIENTS the coefficients of the arguments in your function=0.012 POWERS the powers to which you are raising each of the arguments in your function=1 LABELa label for the action so that its output can be referenced in the input to other actions=Prot_norm PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label Prot_norm calculates the following quantities:
 Quantity   
 Description  
Prot_norm.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=lig_OW_large.lessthan COEFFICIENTS the coefficients of the arguments in your function=0.01351 POWERS the powers to which you are raising each of the arguments in your function=1 LABELa label for the action so that its output can be referenced in the input to other actions=lig_OW_large_norm PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
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The COMBINE action with label lig_OW_large_norm calculates the following quantities:
 Quantity   
 Description  
lig_OW_large_norm.value
a linear compbinationMETADUsed 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=metad
 ARGthe labels of the scalars on which the bias will act=dsb SIGMAthe widths of the Gaussian hills=0.005 HEIGHTthe heights of the Gaussian hills=2.1  BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 PACEthe frequency for hill addition=250
 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=5 GRID_BINthe number of bins for the grid=2000
 REWEIGHTING_NGRID=2000
 REWEIGHTING_NHILLS=20
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialrw: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=300

##Here we some all the bias encountered in the system including restraints+bias on CV##
The REWEIGHT_METAD action with label rw calculates the following quantities:
 Quantity   
 Description  
rw.value
the weight to use for this frame to negate the effect the metadynamics biastbias: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=metad.rbias,funnel.bias,uwall.bias,lwall.bias,rmsdwall.bias,rmsdwallINIT.bias PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label tbias calculates the following quantities:
 Quantity   
 Description  
tbias.value
a linear compbinationPRINTPrint quantities to a file. More details 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_FM STRIDE the frequency with which the quantities of interest should be output=250