PLUMED-NEST

Project ID: plumID:25.022
Source: templates/4MR_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=73-75,940-943,1784,1785
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=2314,2317-2325,2339,2340,2342-2345,2350,2360,2361,2376,2389,2394,2395,2411
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=2315,2316,2318-2321,2326,2329-2337,2352,2362,2372,2373,2387,2401,2406,2407
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=2318,2319,2320,2321
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_1)
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

# Define all possible Zn-N distance pairs in the common window
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 axisd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2318,1744 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2318,1748 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2319,1745 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2319,1749 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2320,1746 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2320,1750 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2321,1747 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2321,1751 NOPBC ignore the periodic boundary conditions when calculating distances

# Define avg of all Zn-N distances
The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsd_Zn_N: DISTANCESCalculate the distances between multiple piars of atoms More details ATOMS1the pairs of atoms that you would like to calculate the angles for=2318,1744 ATOMS2the pairs of atoms that you would like to calculate the angles for=2318,1748 ATOMS3the pairs of atoms that you would like to calculate the angles for=2319,1745 ATOMS4the pairs of atoms that you would like to calculate the angles for=2319,1749 ATOMS5the pairs of atoms that you would like to calculate the angles for=2320,1746 ATOMS6the pairs of atoms that you would like to calculate the angles for=2320,1750 ATOMS7the pairs of atoms that you would like to calculate the angles for=2321,1747 ATOMS8the pairs of atoms that you would like to calculate the angles for=2321,1751 MEAN calculate the mean of all the quantities NOPBC ignore the periodic boundary conditions when calculating distances

# Define lower and upper walls for the adsorbate in axial direction
#lwall_proj: LOWER_WALLS ARG=poa_pore.proj AT=-5 KAPPA=0.75 OFFSET=2.5
#uwall_proj: UPPER_WALLS ARG=poa_pore.proj AT=20 KAPPA=0.75 OFFSET=2.5

# Define upper wall for the adsorbate in non-axial direction
#uwall_ext: UPPER_WALLS ARG=poa_pore.ext AT=3 KAPPA=0.75 OFFSET=0.5

The DISTANCES action with label d_Zn_N calculates the following quantities:
 Quantity   
 Description  
d_Zn_N.mean
the mean of the colvars
d_Zn_N.value
the DISTANCES between the each pair of atoms that were specifiedopes: 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,d_Zn_N.mean
   PACEthe frequency for kernel deposition=250
   BARRIERthe free energy barrier to be overcome=1.0
   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=250*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,d_Zn_N.mean,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
#PRINT ARG=poa_pore.proj,lwall_proj.bias,uwall_proj.bias,poa_pore.ext,uwall_ext.bias FILE=WALL STRIDE=50
ENDPLUMEDTerminate plumed input. More details