PLUMED-NEST

Project ID: plumID:24.001
Source: amylase/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 somethingd_nucThe DISTANCE action with label d_nuc calculates the following quantities:
 Quantity   
 Type   
 Description  
d_nuc
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=3026,7700
d_glyThe DISTANCE action with label d_gly calculates the following quantities:
 Quantity   
 Type   
 Description  
d_gly
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=7700,7699
d_acidThe DISTANCE action with label d_acid calculates the following quantities:
 Quantity   
 Type   
 Description  
d_acid
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=7699,3607


###### Walls #####################
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_nuc ATthe positions of the wall=+4.0 KAPPAthe force constant for the wall=500.0 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_d_nucThe UPPER_WALLS action with label uwall_d_nuc calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_d_nuc.bias
scalar
the instantaneous value of the bias potential
uwall_d_nuc.force2
scalar
the instantaneous value of the squared force due to this bias potential
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_acid ATthe positions of the wall=+4.0 KAPPAthe force constant for the wall=500.0 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_d_acidThe UPPER_WALLS action with label uwall_d_acid calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_d_acid.bias
scalar
the instantaneous value of the bias potential
uwall_d_acid.force2
scalar
the instantaneous value of the squared force due to this bias potential

d_gly-watThe DISTANCE action with label d_gly-wat calculates the following quantities:
 Quantity   
 Type   
 Description  
d_gly-wat
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=7699,26287
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d_gly-wat ATthe positions of the wall=+4.0 KAPPAthe force constant for the wall=500.0 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_d_gly-watThe UPPER_WALLS action with label uwall_d_gly-wat calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall_d_gly-wat.bias
scalar
the instantaneous value of the bias potential
uwall_d_gly-wat.force2
scalar
the instantaneous value of the squared force due to this bias potential

#d_strHbond1: DISTANCE ATOMS=7704,4655
#UPPER_WALLS ARG=d_strHbond1 AT=+2.5 KAPPA=1000.0 EXP=2 LABEL=uwall_d_strHbond1
#d_strHbond2: DISTANCE ATOMS=7708,4654
#UPPER_WALLS ARG=d_strHbond2 AT=+2.5 KAPPA=1000.0 EXP=2 LABEL=uwall_d_strHbond2
##################################


#metad: METAD ARG=d_gly SIGMA=0.1 HEIGHT=2.0 PACE=100 

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=d_gly FUNCthe function you wish to evaluate=step(x-1.8) 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=d_gly,d_acid
  PACEthe frequency for kernel deposition=100
  ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=200
  BARRIERthe free energy barrier to be overcome=50
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  TEMP temperature=300.0
...
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=d_gly,d_acid
  PACEthe frequency for kernel deposition=100
  ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=200
  BARRIERthe free energy barrier to be overcome=50
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  TEMP temperature=300.0
 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=d_gly
 STRIDE the frequency with which the CVs are analyzed=10
 BASIN_LL1List of lower limits for basin #=3.3
 BASIN_UL1List of upper limits for basin #=10.0
... COMMITTOR


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d_gly,d_acid,opes.*,uwall_d_nuc.*,uwall_d_acid.*,uwall_d_gly-wat.* STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR

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