PLUMED-NEST

Project ID: plumID:24.001
Source: chorismate_mutase/opes_flooding_qmmm/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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label  calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
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=5663,5675
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
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=5670,5671

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=+3.60 KAPPAthe force constant for the wall=250.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall_C-C5The UPPER_WALLS action with label uwall_C-C5 calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_C-C5.bias
scalar
the instantaneous value of the bias potential
uwall_C-C5.force2
scalar
the instantaneous value of the squared force due to this bias potential

ddThe COMBINE action with label dd calculates the following quantities:
 Quantity   
 Type   
 Description  
dd
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2 COEFFICIENTS the coefficients of the arguments in your function=1,-1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

chi_excThe CUSTOM action with label chi_exc calculates the following quantities:
 Quantity   
 Type   
 Description  
chi_exc
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dd FUNCthe function you wish to evaluate=step(-x+0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=dd
  PACEthe frequency for kernel deposition=100
  ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=200
  BARRIERthe free energy barrier to be overcome=45
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  TEMP temperature=300.0
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=RESTART_INFO
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=100
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=dd
  PACEthe frequency for kernel deposition=100
  ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=200
  BARRIERthe free energy barrier to be overcome=45
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  TEMP temperature=300.0
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=RESTART_INFO
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=100
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...

COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=dd
 STRIDE the frequency with which the CVs are analyzed=10
 BASIN_LL1List of lower limits for basin #=-10.0
 BASIN_UL1List of upper limits for basin #=-2.0
... COMMITTOR

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,dd,opes.*,uwall_C-C5.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1

FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1