PLUMED-NEST

Project ID: plumID:25.025
Source: tal1/opes_mw/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

# --- (OPES Multi-Walker) ---

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 potentialOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opes
   ARGthe labels of the scalars on which the bias will act=c1_cpdb,fps.lp
   BARRIERthe free energy barrier to be overcome=50
   PACEthe frequency for kernel deposition=500
   FILE a file in which the list of all deposited kernels is stored=../KERNELS
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=../compressed_KERNELS
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=../compressed_KERNELS
   STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=50000
   WALKERS_MPI switch on MPI version of multiple walkers
... OPES_METAD

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the biasPRINTPrint 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.*,opes.*,fps.*,funnel.* 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