PLUMED-NEST

Project ID: plumID:23.028
Source: DeepMD_simulations/Unbiased/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=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A
The UNITS action with label  calculates somethingH: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,377,378,379,380,381,384,386,387,388,390,391,392

The GROUP action with label H calculates somethingN: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,372,373,374,375,376,383,385,389

The GROUP action with label N calculates somethingLi: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,37,38,39,40,41,42,43,44,45,46,47,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,149,150,151,152,153,154,155,156,157,158,169,170,171,172,173,174,175,176,177,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,212,213,214,215,216,217,224,225,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,362,363,364,365,366,367,368,369,370,371,382

The GROUP action with label Li calculates somethingghosta: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=0,0,15

The FIXEDATOM action with label ghosta calculates somethingene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingdis_GH: 
ZDISTANCES
Calculate the z components of the vectors connecting one or many pairs of atoms. More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=ghosta 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H 
MAX
calculate the maximum value
={BETA=0.5}
The ZDISTANCES action with label dis_GH calculates somethinguwall1: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dis_GH.max 
AT
the positions of the wall
=12.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2
The UPPER_WALLS action with label uwall1 calculates somethingdis_GN: 
ZDISTANCES
Calculate the z components of the vectors connecting one or many pairs of atoms. More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=ghosta 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=N 
MAX
calculate the maximum value
={BETA=0.5}
The ZDISTANCES action with label dis_GN calculates somethinguwall2: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=dis_GN.max 
AT
the positions of the wall
=12.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2

The UPPER_WALLS action with label uwall2 calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=1000
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=4000