PLUMED-NEST

Project ID: plumID:25.025
Source: tal1/wt-metad/template/plumed.dat
Originally used with PLUMED version: 2.11
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

# --- ATOMS DEFINITIONS and ALIGNMENT ---

RNA_mol: 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=1-1065 
The GROUP action with label RNA_mol calculates somethinglig_mol: 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=1068-1088
The GROUP action with label lig_mol 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=RNA_mol
The WHOLEMOLECULES action with label  calculates somethinganchor_atom: 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=902
The GROUP action with label anchor_atom calculates somethingWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=lig_mol AROUNDreference atoms=anchor_atom GROUPBY group atoms so as not to break molecules=21

# ------ (CPDb index for C27) ------

p1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=240-251,819-833,177-187,884-897
The CENTER action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.value
the position of the center of massp1_new: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=177-187,884-897
The CENTER action with label p1_new calculates the following quantities:
 Quantity   
 Description  
p1_new.value
the position of the center of massp4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=853,854,856,858,862,863
The CENTER action with label p4 calculates the following quantities:
 Quantity   
 Description  
p4.value
the position of the center of massp2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=840-844
The CENTER action with label p2 calculates the following quantities:
 Quantity   
 Description  
p2.value
the position of the center of massp3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=871-875
The CENTER action with label p3 calculates the following quantities:
 Quantity   
 Description  
p3.value
the position of the center of massc1_cpdb: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=p1,p2,p3,p4
The TORSION action with label c1_cpdb calculates the following quantities:
 Quantity   
 Description  
c1_cpdb.value
the TORSION involving these atomsc1_mod: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=p1_new,p2,p3,p4
# ----- (Modification of CPDb to avoid periodicity) ----
The TORSION action with label c1_mod calculates the following quantities:
 Quantity   
 Description  
c1_mod.value
the TORSION involving these atomsc1_nopbc: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c1_cpdb FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label c1_nopbc calculates the following quantities:
 Quantity   
 Description  
c1_nopbc.value
an arbitrary functionc1_new: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c1_nopbc FUNCthe function you wish to evaluate=x+1.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-pi,pi
The CUSTOM action with label c1_new calculates the following quantities:
 Quantity   
 Description  
c1_new.value
an arbitrary functionc1_new_nopbc: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c1_new FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# -------(CPDb walls)--------

The CUSTOM action with label c1_new_nopbc calculates the following quantities:
 Quantity   
 Description  
c1_new_nopbc.value
an arbitrary functionLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=c1_new_nopbc ATthe positions of the wall=-2.5 KAPPAthe force constant for the wall=10000 LABELa label for the action so that its output can be referenced in the input to other actions=wl
The LOWER_WALLS action with label wl calculates the following quantities:
 Quantity   
 Description  
wl.bias
the instantaneous value of the bias potential
wl.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=c1_new_nopbc ATthe positions of the wall=2 KAPPAthe force constant for the wall=10000 LABELa label for the action so that its output can be referenced in the input to other actions=wu

# -------(rmsd) ------

#drmsd: DRMSD REFERENCE=c1_p_from_processed.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=1.5
The UPPER_WALLS action with label wu calculates the following quantities:
 Quantity   
 Description  
wu.bias
the instantaneous value of the bias potential
wu.force2
the instantaneous value of the squared force due to this bias potentialrmsd: 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=c1_p_from_processed.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# ------- (rmsd wall) -------

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=0.4 KAPPAthe force constant for the wall=15000 LABELa label for the action so that its output can be referenced in the input to other actions=wu_rmsd

#-------- (Hbond coordination number) ----

#C22_N4: GROUP ATOMS=700
#C22_N3: GROUP ATOMS=703
#U24_N3: GROUP ATOMS=762
#MOL_O2: GROUP ATOMS=1075
#MOL_N3: GROUP ATOMS=1076
#MOL_N4: GROUP ATOMS=1078

#cord_n1: COORDINATION GROUPA=MOL_O2 GROUPB=C22_N4 SWITCH={RATIONAL D_0=0.0 R_0=0.5 NN=6 MM=10 D_MAX=1.3} NLIST NL_CUTOFF=1.4 NL_STRIDE=5
#cord_n2: COORDINATION GROUPA=MOL_N3 GROUPB=C22_N3 SWITCH={RATIONAL D_0=0.0 R_0=0.5 NN=6 MM=10 D_MAX=1.3} NLIST NL_CUTOFF=1.4 NL_STRIDE=5
#cord_n3: COORDINATION GROUPA=MOL_N4 GROUPB=U24_N3 SWITCH={RATIONAL D_0=0.0 R_0=0.5 NN=6 MM=10 D_MAX=1.3} NLIST NL_CUTOFF=1.4 NL_STRIDE=5
#cord_all: MATHEVAL ARG=cord_n1,cord_n2,cord_n3 VAR=x,y,z FUNC=(x+y+z)/3 PERIODIC=NO

# ----- (RNA and LIG COM) ----

The UPPER_WALLS action with label wu_rmsd calculates the following quantities:
 Quantity   
 Description  
wu_rmsd.bias
the instantaneous value of the bias potential
wu_rmsd.force2
the instantaneous value of the squared force due to this bias potentialbp_com: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=195,228,175,205,238,269,692,723,753,817,882,915 #atoms within a range of binding pocket
The CENTER action with label bp_com calculates the following quantities:
 Quantity   
 Description  
bp_com.value
the position of the center of masslig_group: 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=1068-1088

#-------- (water coordination) ----

The GROUP action with label lig_group calculates somethingWO: 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=1186-40609:4
The GROUP action with label WO calculates somethingwat_cn_1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=bp_com GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label wat_cn_1 calculates the following quantities:
 Quantity   
 Description  
wat_cn_1.value
the value of the coordinationwat_cn_2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=lig_group GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.3} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5

# ----- (funnel) -------

The COORDINATION action with label wat_cn_2 calculates the following quantities:
 Quantity   
 Description  
wat_cn_2.value
the value of the coordinationlig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081
The COM action with label 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=lig REFERENCEa file in pdb format containing the structure you would like to align=c1_p_from_processed.pdb ANCHORClosest protein atom to the ligand, picked to avoid pbc problems during the simulation=902 POINTS6 values defining x, y, and z of the 2 points used to construct the line=2.911,4.049,4.242,2.633,4.503,4.697
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=1.5 ALPHAangle to change the width of the cone section=0.65 RCYLradius of the cylindrical section=0.2 MINSminimum value assumed by fps=-3.0 MAXS maximum value assumed by fps=5.0 KAPPAconstant to be used for the funnel-shape restraint potential=50000 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
The FUNNEL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.bias
the instantaneous value of the 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=0.6 KAPPAthe force constant for the wall=5000 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=2.8 KAPPAthe force constant for the wall=5000 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

# --- (Metadynamics) ---

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 potentialMETADUsed 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=c1_cpdb,fps.lp
   PACEthe frequency for hill addition=500
   HEIGHTthe heights of the Gaussian hills=1.2
   SIGMAthe widths of the Gaussian hills=0.05,0.05
   BIASFACTORuse well tempered metadynamics and use this bias factor=10
...

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialCOMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=fps.lp
 STRIDE the frequency with which the CVs are analyzed=10
 BASIN_LL1List of lower limits for basin #=2.5
 BASIN_UL1List of upper limits for basin #=3.0
... COMMITTOR

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1_cpdb,c1_mod,c1_new,wl.*,wu.*,wu_rmsd.*,wat_cn_1,wat_cn_2,lwall.*,uwall.*,metad.*,fps.* 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 FMT the format that should be used to output real numbers=%8.4f