PLUMED-NEST

Project ID: plumID:23.017
Source: classical_unbiased_MD/unbiasedCVs/plumed.dat
Originally used with PLUMED version: 2.9
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 ---
proteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
atoms
indices of atoms specified in 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=1-7654
WHOLEMOLECULESThis 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=protein
The WHOLEMOLECULES action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=npt_eqm3_align2z_CA.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL


# --- Distance DESCRIPTOR ---
D197CAThe GROUP action with label D197CA calculates the following quantities:
 Quantity   
 Type   
 Description  
D197CA
atoms
indices of atoms specified in 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=3020
active_ligThe CENTER_FAST action with label active_lig calculates the following quantities:
 Quantity   
 Type   
 Description  
active_lig
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=7698-7719  #The reactive rings of the ligand (residue 500-O4 and whole residue 501)
D_nu-ligThe DISTANCE action with label D_nu-lig calculates the following quantities:
 Quantity   
 Type   
 Description  
D_nu-lig
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=D197CA,active_lig
#D_nu-lig: DISTANCE ATOMS=D197CA,active_lig COMPONENTS


# --- Water CN around active part of the ligand ---
WOThe GROUP action with label WO calculates the following quantities:
 Quantity   
 Type   
 Description  
WO
atoms
indices of atoms specified in 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=7765-67992:3  #water molecules

waterCNThe COORDINATION action with label waterCN calculates the following quantities:
 Quantity   
 Type   
 Description  
waterCN
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=active_lig 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=0.6 NN=10 MM=20 D_MAX=0.7} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20


PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1 ARGthe labels of the values that you would like to print to the file=D_nu-lig,waterCN FILEthe name of the file on which to output these quantities=distance_waterCN_unbiased FMTthe format that should be used to output real numbers=%8.4f