PLUMED-NEST

Project ID: plumID:23.030
Source: T4L_benzene/opes_flooding/template_barr30/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

WHOLEMOLECULESThis 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=1-2593 ENTITY1the atoms that make up a molecule that you wish to align=2594-2605
The WHOLEMOLECULES action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=heavy_atoms.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# Group definition
prot_nohThe GROUP action with label prot_noh calculates the following quantities:
 Quantity   
 Type   
 Description  
prot_noh
atoms
indices of atoms specified in GROUP: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
sphThe GROUP action with label sph calculates the following quantities:
 Quantity   
 Type   
 Description  
sph
atoms
indices of atoms specified in GROUP: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=sphere
bnzThe GROUP action with label bnz calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz
atoms
indices of atoms specified in GROUP: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=BNZ_noH

WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=bnz AROUNDreference atoms=sph

sph_centerThe COM action with label sph_center calculates the following quantities:
 Quantity   
 Type   
 Description  
sph_center
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=sph
bnz_centerThe COM action with label bnz_center calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz_center
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=bnz

sph_coordThe POSITION action with label sph_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
sph_coord.x
scalar
the x-component of the atom position
sph_coord.y
scalar
the y-component of the atom position
sph_coord.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=sph_center NOPBC ignore the periodic boundary conditions when calculating distances
bnz_coordThe POSITION action with label bnz_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz_coord.x
scalar
the x-component of the atom position
bnz_coord.y
scalar
the y-component of the atom position
bnz_coord.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=bnz_center NOPBC ignore the periodic boundary conditions when calculating distances

abs_xThe MATHEVAL action with label abs_x calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_x
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=bnz_coord.x,sph_coord.x FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abs_yThe MATHEVAL action with label abs_y calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_y
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=bnz_coord.y,sph_coord.y FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abs_zThe MATHEVAL action with label abs_z calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_z
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=bnz_coord.z,sph_coord.z FUNCthe function you wish to evaluate=x-y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

rhoThe MATHEVAL action with label rho calculates the following quantities:
 Quantity   
 Type   
 Description  
rho
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_x,abs_y,abs_z FUNCthe function you wish to evaluate=sqrt(x*x+y*y+z*z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
thetaThe MATHEVAL action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_z,rho FUNCthe function you wish to evaluate=acos(x/y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=0.,pi
phiThe MATHEVAL action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=abs_x,abs_y FUNCthe function you wish to evaluate=atan2(y,x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-pi,pi


# Coordination number
cThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=bnz GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=prot_noh R_0The r_0 parameter of the switching function=0.45
c: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=bnz GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=prot_noh R_0The r_0 parameter of the switching function=0.45  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0


#OPES Flooding
targetThe CUSTOM action with label target calculates the following quantities:
 Quantity   
 Type   
 Description  
target
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=rho FUNCthe function you wish to evaluate=step(x-0.9) 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=rho,c
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=30
  TEMP temperature=300.0
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=target
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
...
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=rho,c
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=30
  TEMP temperature=300.0
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=target
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
 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=rho
  STRIDE the frequency with which the CVs are analyzed=1000
  BASIN_LL1List of lower limits for basin #=2.5
  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=rho,theta,phi,c,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=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=opes.bias FILEthe name of the file on which to output these quantities=COLVARb STRIDE the frequency with which the quantities of interest should be output=10


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=500