PLUMED-NEST

Project ID: plumID:25.022
Source: templates/6MR_diffusion/plumed.dat
Originally used with PLUMED version: 2.8.2
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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=eV

The UNITS action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=reference_structure.pdb

# Define the adsorbate (guest) as a whole molecule
adsorbate_atoms: 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=73,74,75,652,653,654,655,1208,1209
The GROUP action with label adsorbate_atoms 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=adsorbate_atoms
adsorbate: 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=adsorbate_atoms NOPBC ignore the periodic boundary conditions when calculating distances MASS calculate the center of mass

# Define the left pore (first cavity) as a whole molecule
The CENTER action with label adsorbate calculates the following quantities:
 Quantity   
 Description  
adsorbate.value
the position of the center of massleft_pore_atoms: 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=1546-1548,1550-1557,1561,1566-1569,1571,1574,1576,1585,1594,1596,1599,1601
The GROUP action with label left_pore_atoms calculates somethingleft_pore: 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=left_pore_atoms NOPBC ignore the periodic boundary conditions when calculating distances MASS calculate the center of mass

# Define the right pore (second cavity) as a whole molecule
The CENTER action with label left_pore calculates the following quantities:
 Quantity   
 Description  
left_pore.value
the position of the center of massright_pore_atoms: 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=1547-1549,1551,1552,1555,1556,1558,1563,1564,1572,1577,1578,1580,1582,1589,1595,1597,1598,1603,1605,1610,1626,1629
The GROUP action with label right_pore_atoms calculates somethingright_pore: 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=right_pore_atoms NOPBC ignore the periodic boundary conditions when calculating distances MASS calculate the center of mass

# Define the common window between both the left and right pores
The CENTER action with label right_pore calculates the following quantities:
 Quantity   
 Description  
right_pore.value
the position of the center of masscommon_window_atoms: 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=1547,1548,1551,1552,1555,1556
The GROUP action with label common_window_atoms calculates somethingcommon_window: 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=common_window_atoms NOPBC ignore the periodic boundary conditions when calculating distances MASS calculate the center of mass

# Define an axis between the common window COM and the right pore COM (useful for tracking the adsorbate)
The CENTER action with label common_window calculates the following quantities:
 Quantity   
 Description  
common_window.value
the position of the center of masspoa_right: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=common_window,right_pore ATOMThe atom whose position we want to project on the axis of interest=adsorbate NOPBC ignore the periodic boundary conditions when calculating distances

# Define an axis between the left pore COM and the right pore COM (BIAS CV)
The PROJECTION_ON_AXIS action with label poa_right calculates the following quantities:
 Quantity   
 Description  
poa_right.value
the value of the projection along the axispoa_pore: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=left_pore,right_pore ATOMThe atom whose position we want to project on the axis of interest=adsorbate NOPBC ignore the periodic boundary conditions when calculating distances

The PROJECTION_ON_AXIS action with label poa_pore calculates the following quantities:
 Quantity   
 Description  
poa_pore.value
the value of the projection along the axisopes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
   FILE a file in which the list of all deposited kernels is stored=Kernels.data
   TEMP temperature=300.0
   ARGthe labels of the scalars on which the bias will act=poa_pore.proj
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=0.3
   SIGMA the initial widths of the kernels=0.30
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
   STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500*1000
   STORE_STATES append to STATE_WFILE instead of ovewriting it each time
...

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=poa_pore.proj,poa_right.proj,opes.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=50
ENDPLUMEDTerminate plumed input. More details