PLUMED-NEST

Project ID: plumID:23.015
Source: OPEX_and_METAD/github_opex_80d/plumed.dat
Originally used with PLUMED version: 2.8
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=1-280 ENTITY1the atoms that make up a molecule that you wish to align=281-560

The WHOLEMOLECULES action with label  calculates somethingc1The COM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
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=1-25
c2The COM action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
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=281-305

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
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=c1,c2

OWThe GROUP action with label OW calculates the following quantities:
 Quantity   
 Type   
 Description  
OW
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 ATOMSthe numerical indexes for the set of atoms in the group=561-40352:3
cn1The COORDINATION action with label cn1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500
cn1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
cn2The COORDINATION action with label cn2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn2
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500
cn2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=OW R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =12 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=500  D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function; 0 implies 2*NN=0
cnaThe CUSTOM action with label cna calculates the following quantities:
 Quantity   
 Type   
 Description  
cna
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cn1,cn2 FUNCthe function you wish to evaluate=0.5*(x+y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

metadThe OPES_METAD_EXPLORE action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
metad.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
metad.neff
scalar
effective sample size
metad.nker
scalar
total number of compressed kernels used to represent the bias
metad.nlker
scalar
number of kernels in the neighbor list
metad.nlsteps
scalar
number of steps from last neighbor list update: OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
   ARGthe labels of the scalars on which the bias will act=d,cna
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=50
   FILE a file in which the list of all deposited kernels is stored=kernals.data
   WALKERS_MPI switch on MPI version of multiple walkers
   NLIST use neighbor list for kernels summation, faster but experimental
...
metad: OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
   ARGthe labels of the scalars on which the bias will act=d,cna
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=50
   FILE a file in which the list of all deposited kernels is stored=kernals.data
   WALKERS_MPI switch on MPI version of multiple walkers
   NLIST use neighbor list for kernels summation, faster but experimental
 TEMP temperature=-1 SIGMA the initial widths of the kernels, divided by the square root of gamma=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...

UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=3.5 KAPPAthe force constant for the wall=10000
LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=1.2 KAPPAthe force constant for the wall=10000

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=Colvar.data ARGthe labels of the values that you would like to print to the file=*