PLUMED-NEST

Project ID: plumID:23.028
Source: AIMD_simulation/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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label  calculates somethingH: 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=9,10,11,12,13,14,15,16,27,28,31,32,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,147,148,149,150,155,156,157,158,161,162,167,168,169,170,175,176,177,178,181,182,183,184,189,190,191,192,197,198,258,259,260
The GROUP action with label H calculates somethingN: 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=17,18,19,20,21,22,23,24,25,26,29,30,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,151,152,153,154,159,160,163,164,165,166,171,172,173,174,179,180,185,186,187,188,193,194,195,196,199,200,201,202,257
The GROUP action with label N calculates somethingLi: 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=1-8:1,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256

The GROUP action with label Li calculates somethingene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingmax_H: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=H SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Li,N SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.05}

The COORDINATIONNUMBER action with label max_H calculates the following quantities:
 Quantity   
 Description  
max_H.max
the maximum colvar
max_H.value
the coordination numbers of the specified atomsghosta: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,0,20
The FIXEDATOM action with label ghosta calculates somethingNH3c: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=257-260
The COM action with label NH3c calculates somethingdNH3hosta: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ghosta,NH3c COMPONENTS calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label dNH3hosta calculates the following quantities:
 Quantity   
 Description  
dNH3hosta.x
the x-component of the vector connecting the two atoms
dNH3hosta.y
the y-component of the vector connecting the two atoms
dNH3hosta.z
the z-component of the vector connecting the two atoms
dNH3hosta.value
the DISTANCE between this pair of atomsabs_dNH3hostaz: 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=dNH3hosta.z FUNCthe function you wish to evaluate=abs(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label abs_dNH3hostaz calculates the following quantities:
 Quantity   
 Description  
abs_dNH3hostaz.value
an arbitrary functionuwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=abs_dNH3hostaz ATthe positions of the wall=11.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2 

The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentialOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ... 
LABELa label for the action so that its output can be referenced in the input to other actions=opes2
ARGthe labels of the scalars on which the bias will act=max_H.max 
PACEthe frequency for kernel deposition=50
BARRIERthe free energy barrier to be overcome=100 # #BIASFACTOR=20 # #KERNEL_CUTOFF=7.5 
TEMP temperature=750
... OPES_METAD

The OPES_METAD action with label opes2 calculates the following quantities:
 Quantity   
 Description  
opes2.bias
the instantaneous value of the bias potential
opes2.rct
estimate of c(t)
opes2.zed
estimate of Z_n
opes2.neff
effective sample size
opes2.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=* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=2
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=2