PLUMED-NEST-TEST-SITE

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 ---
protein: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-7654
The GROUP action with label protein calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=protein
The WHOLEMOLECULES action with label  calculates something
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
REFERENCE
a 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 ---
D197CA: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=3020
The GROUP action with label D197CA calculates somethingactive_lig: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the 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)
The CENTER action with label active_lig calculates the following quantities:
 Quantity   
 Description  
active_lig.value
the position of the center of massD_nu-lig: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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 ---
The DISTANCE action with label D_nu-lig calculates the following quantities:
 Quantity   
 Description  
D_nu-lig.value
the DISTANCE between this pair of atomsWO: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=7765-67992:3  #water molecules

The GROUP action with label WO calculates somethingwaterCN: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=active_lig 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={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_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20


The COORDINATION action with label waterCN calculates the following quantities:
 Quantity   
 Description  
waterCN.value
the value of the coordination
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
ARG
the input for this action is the scalar output from one or more other actions
=D_nu-lig,waterCN 
FILE
the name of the file on which to output these quantities
=distance_waterCN_unbiased 
FMT
the format that should be used to output real numbers
=%8.4f