PLUMED-NEST

Project ID: plumID:21.038
Source: UreaNucleationFromMelt/chi4.dat
Originally used with PLUMED version: 2.6.1
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

# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=PairOrientationalEntropy.cpp
The LOAD action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=ManyAngle2_ST.cpp


# Define groups for the CV
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=centers.dat
# The command:
# INCLUDE FILE=centers.dat
# ensures PLUMED loads the contents of the file called centers.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label centers.dat calculates somethingc1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3,6
The CENTER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the position of the center of massc2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=11,14
The CENTER action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the position of the center of massc3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=19,22
The CENTER action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.value
the position of the center of massc4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=27,30
The CENTER action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.value
the position of the center of massc5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=35,38
The CENTER action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.value
the position of the center of massc6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=43,46
The CENTER action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.value
the position of the center of massc7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=51,54
The CENTER action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.value
the position of the center of massc8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=59,62
The CENTER action with label c8 calculates the following quantities:
 Quantity   
 Description  
c8.value
the position of the center of massc9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=67,70
The CENTER action with label c9 calculates the following quantities:
 Quantity   
 Description  
c9.value
the position of the center of massc10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=75,78
The CENTER action with label c10 calculates the following quantities:
 Quantity   
 Description  
c10.value
the position of the center of massc11: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=83,86
The CENTER action with label c11 calculates the following quantities:
 Quantity   
 Description  
c11.value
the position of the center of massc12: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=91,94
The CENTER action with label c12 calculates the following quantities:
 Quantity   
 Description  
c12.value
the position of the center of massc13: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=99,102
The CENTER action with label c13 calculates the following quantities:
 Quantity   
 Description  
c13.value
the position of the center of massc14: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=107,110
The CENTER action with label c14 calculates the following quantities:
 Quantity   
 Description  
c14.value
the position of the center of massc15: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=115,118
The CENTER action with label c15 calculates the following quantities:
 Quantity   
 Description  
c15.value
the position of the center of massc16: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=123,126
The CENTER action with label c16 calculates the following quantities:
 Quantity   
 Description  
c16.value
the position of the center of massc17: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=131,134
The CENTER action with label c17 calculates the following quantities:
 Quantity   
 Description  
c17.value
the position of the center of massc18: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=139,142
The CENTER action with label c18 calculates the following quantities:
 Quantity   
 Description  
c18.value
the position of the center of massc19: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=147,150
The CENTER action with label c19 calculates the following quantities:
 Quantity   
 Description  
c19.value
the position of the center of massc20: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=155,158
The CENTER action with label c20 calculates the following quantities:
 Quantity   
 Description  
c20.value
the position of the center of massc21: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=163,166
The CENTER action with label c21 calculates the following quantities:
 Quantity   
 Description  
c21.value
the position of the center of massc22: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=171,174
The CENTER action with label c22 calculates the following quantities:
 Quantity   
 Description  
c22.value
the position of the center of massc23: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=179,182
The CENTER action with label c23 calculates the following quantities:
 Quantity   
 Description  
c23.value
the position of the center of massc24: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=187,190
The CENTER action with label c24 calculates the following quantities:
 Quantity   
 Description  
c24.value
the position of the center of massc25: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=195,198
The CENTER action with label c25 calculates the following quantities:
 Quantity   
 Description  
c25.value
the position of the center of massc26: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=203,206
The CENTER action with label c26 calculates the following quantities:
 Quantity   
 Description  
c26.value
the position of the center of massc27: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=211,214
The CENTER action with label c27 calculates the following quantities:
 Quantity   
 Description  
c27.value
the position of the center of massc28: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=219,222
The CENTER action with label c28 calculates the following quantities:
 Quantity   
 Description  
c28.value
the position of the center of massc29: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=227,230
The CENTER action with label c29 calculates the following quantities:
 Quantity   
 Description  
c29.value
the position of the center of massc30: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=235,238
The CENTER action with label c30 calculates the following quantities:
 Quantity   
 Description  
c30.value
the position of the center of massc31: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=243,246
The CENTER action with label c31 calculates the following quantities:
 Quantity   
 Description  
c31.value
the position of the center of massc32: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=251,254
The CENTER action with label c32 calculates the following quantities:
 Quantity   
 Description  
c32.value
the position of the center of massc33: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=259,262
The CENTER action with label c33 calculates the following quantities:
 Quantity   
 Description  
c33.value
the position of the center of massc34: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=267,270
The CENTER action with label c34 calculates the following quantities:
 Quantity   
 Description  
c34.value
the position of the center of massc35: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=275,278
The CENTER action with label c35 calculates the following quantities:
 Quantity   
 Description  
c35.value
the position of the center of massc36: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=283,286
The CENTER action with label c36 calculates the following quantities:
 Quantity   
 Description  
c36.value
the position of the center of massc37: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=291,294
The CENTER action with label c37 calculates the following quantities:
 Quantity   
 Description  
c37.value
the position of the center of massc38: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=299,302
The CENTER action with label c38 calculates the following quantities:
 Quantity   
 Description  
c38.value
the position of the center of massc39: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=307,310
The CENTER action with label c39 calculates the following quantities:
 Quantity   
 Description  
c39.value
the position of the center of massc40: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=315,318
The CENTER action with label c40 calculates the following quantities:
 Quantity   
 Description  
c40.value
the position of the center of massc41: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=323,326
The CENTER action with label c41 calculates the following quantities:
 Quantity   
 Description  
c41.value
the position of the center of massc42: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=331,334
The CENTER action with label c42 calculates the following quantities:
 Quantity   
 Description  
c42.value
the position of the center of massc43: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=339,342
The CENTER action with label c43 calculates the following quantities:
 Quantity   
 Description  
c43.value
the position of the center of massc44: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=347,350
The CENTER action with label c44 calculates the following quantities:
 Quantity   
 Description  
c44.value
the position of the center of massc45: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=355,358
The CENTER action with label c45 calculates the following quantities:
 Quantity   
 Description  
c45.value
the position of the center of massc46: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=363,366
The CENTER action with label c46 calculates the following quantities:
 Quantity   
 Description  
c46.value
the position of the center of massc47: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=371,374
The CENTER action with label c47 calculates the following quantities:
 Quantity   
 Description  
c47.value
the position of the center of massc48: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=379,382
The CENTER action with label c48 calculates the following quantities:
 Quantity   
 Description  
c48.value
the position of the center of massc49: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=387,390
The CENTER action with label c49 calculates the following quantities:
 Quantity   
 Description  
c49.value
the position of the center of massc50: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=395,398
The CENTER action with label c50 calculates the following quantities:
 Quantity   
 Description  
c50.value
the position of the center of massc51: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=403,406
The CENTER action with label c51 calculates the following quantities:
 Quantity   
 Description  
c51.value
the position of the center of massc52: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=411,414
The CENTER action with label c52 calculates the following quantities:
 Quantity   
 Description  
c52.value
the position of the center of massc53: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=419,422
The CENTER action with label c53 calculates the following quantities:
 Quantity   
 Description  
c53.value
the position of the center of massc54: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=427,430
The CENTER action with label c54 calculates the following quantities:
 Quantity   
 Description  
c54.value
the position of the center of massc55: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=435,438
The CENTER action with label c55 calculates the following quantities:
 Quantity   
 Description  
c55.value
the position of the center of massc56: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=443,446
The CENTER action with label c56 calculates the following quantities:
 Quantity   
 Description  
c56.value
the position of the center of massc57: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=451,454
The CENTER action with label c57 calculates the following quantities:
 Quantity   
 Description  
c57.value
the position of the center of massc58: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=459,462
The CENTER action with label c58 calculates the following quantities:
 Quantity   
 Description  
c58.value
the position of the center of massc59: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=467,470
The CENTER action with label c59 calculates the following quantities:
 Quantity   
 Description  
c59.value
the position of the center of massc60: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=475,478
The CENTER action with label c60 calculates the following quantities:
 Quantity   
 Description  
c60.value
the position of the center of massc61: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=483,486
The CENTER action with label c61 calculates the following quantities:
 Quantity   
 Description  
c61.value
the position of the center of massc62: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=491,494
The CENTER action with label c62 calculates the following quantities:
 Quantity   
 Description  
c62.value
the position of the center of massc63: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=499,502
The CENTER action with label c63 calculates the following quantities:
 Quantity   
 Description  
c63.value
the position of the center of massc64: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=507,510
The CENTER action with label c64 calculates the following quantities:
 Quantity   
 Description  
c64.value
the position of the center of massc65: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=515,518
The CENTER action with label c65 calculates the following quantities:
 Quantity   
 Description  
c65.value
the position of the center of massc66: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=523,526
The CENTER action with label c66 calculates the following quantities:
 Quantity   
 Description  
c66.value
the position of the center of massc67: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=531,534
The CENTER action with label c67 calculates the following quantities:
 Quantity   
 Description  
c67.value
the position of the center of massc68: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=539,542
The CENTER action with label c68 calculates the following quantities:
 Quantity   
 Description  
c68.value
the position of the center of massc69: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=547,550
The CENTER action with label c69 calculates the following quantities:
 Quantity   
 Description  
c69.value
the position of the center of massc70: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=555,558
The CENTER action with label c70 calculates the following quantities:
 Quantity   
 Description  
c70.value
the position of the center of massc71: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=563,566
The CENTER action with label c71 calculates the following quantities:
 Quantity   
 Description  
c71.value
the position of the center of massc72: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=571,574
The CENTER action with label c72 calculates the following quantities:
 Quantity   
 Description  
c72.value
the position of the center of massc73: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=579,582
The CENTER action with label c73 calculates the following quantities:
 Quantity   
 Description  
c73.value
the position of the center of massc74: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=587,590
The CENTER action with label c74 calculates the following quantities:
 Quantity   
 Description  
c74.value
the position of the center of massc75: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=595,598
The CENTER action with label c75 calculates the following quantities:
 Quantity   
 Description  
c75.value
the position of the center of massc76: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=603,606
The CENTER action with label c76 calculates the following quantities:
 Quantity   
 Description  
c76.value
the position of the center of massc77: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=611,614
The CENTER action with label c77 calculates the following quantities:
 Quantity   
 Description  
c77.value
the position of the center of massc78: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=619,622
The CENTER action with label c78 calculates the following quantities:
 Quantity   
 Description  
c78.value
the position of the center of massc79: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=627,630
The CENTER action with label c79 calculates the following quantities:
 Quantity   
 Description  
c79.value
the position of the center of massc80: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=635,638
The CENTER action with label c80 calculates the following quantities:
 Quantity   
 Description  
c80.value
the position of the center of massc81: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=643,646
The CENTER action with label c81 calculates the following quantities:
 Quantity   
 Description  
c81.value
the position of the center of massc82: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=651,654
The CENTER action with label c82 calculates the following quantities:
 Quantity   
 Description  
c82.value
the position of the center of massc83: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=659,662
The CENTER action with label c83 calculates the following quantities:
 Quantity   
 Description  
c83.value
the position of the center of massc84: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=667,670
The CENTER action with label c84 calculates the following quantities:
 Quantity   
 Description  
c84.value
the position of the center of massc85: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=675,678
The CENTER action with label c85 calculates the following quantities:
 Quantity   
 Description  
c85.value
the position of the center of massc86: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=683,686
The CENTER action with label c86 calculates the following quantities:
 Quantity   
 Description  
c86.value
the position of the center of massc87: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=691,694
The CENTER action with label c87 calculates the following quantities:
 Quantity   
 Description  
c87.value
the position of the center of massc88: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=699,702
The CENTER action with label c88 calculates the following quantities:
 Quantity   
 Description  
c88.value
the position of the center of massc89: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=707,710
The CENTER action with label c89 calculates the following quantities:
 Quantity   
 Description  
c89.value
the position of the center of massc90: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=715,718
The CENTER action with label c90 calculates the following quantities:
 Quantity   
 Description  
c90.value
the position of the center of massc91: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=723,726
The CENTER action with label c91 calculates the following quantities:
 Quantity   
 Description  
c91.value
the position of the center of massc92: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=731,734
The CENTER action with label c92 calculates the following quantities:
 Quantity   
 Description  
c92.value
the position of the center of massc93: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=739,742
The CENTER action with label c93 calculates the following quantities:
 Quantity   
 Description  
c93.value
the position of the center of massc94: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=747,750
The CENTER action with label c94 calculates the following quantities:
 Quantity   
 Description  
c94.value
the position of the center of massc95: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=755,758
The CENTER action with label c95 calculates the following quantities:
 Quantity   
 Description  
c95.value
the position of the center of massc96: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=763,766
The CENTER action with label c96 calculates the following quantities:
 Quantity   
 Description  
c96.value
the position of the center of massc97: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=771,774
The CENTER action with label c97 calculates the following quantities:
 Quantity   
 Description  
c97.value
the position of the center of massc98: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=779,782
The CENTER action with label c98 calculates the following quantities:
 Quantity   
 Description  
c98.value
the position of the center of massc99: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=787,790
The CENTER action with label c99 calculates the following quantities:
 Quantity   
 Description  
c99.value
the position of the center of massc100: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=795,798
The CENTER action with label c100 calculates the following quantities:
 Quantity   
 Description  
c100.value
the position of the center of massc101: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=803,806
The CENTER action with label c101 calculates the following quantities:
 Quantity   
 Description  
c101.value
the position of the center of massc102: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=811,814
The CENTER action with label c102 calculates the following quantities:
 Quantity   
 Description  
c102.value
the position of the center of massc103: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=819,822
The CENTER action with label c103 calculates the following quantities:
 Quantity   
 Description  
c103.value
the position of the center of massc104: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=827,830
The CENTER action with label c104 calculates the following quantities:
 Quantity   
 Description  
c104.value
the position of the center of massc105: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=835,838
The CENTER action with label c105 calculates the following quantities:
 Quantity   
 Description  
c105.value
the position of the center of massc106: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=843,846
The CENTER action with label c106 calculates the following quantities:
 Quantity   
 Description  
c106.value
the position of the center of massc107: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=851,854
The CENTER action with label c107 calculates the following quantities:
 Quantity   
 Description  
c107.value
the position of the center of massc108: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=859,862

The CENTER action with label c108 calculates the following quantities:
 Quantity   
 Description  
c108.value
the position of the center of massNcenter: 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=c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c18,c19,c20,c21,c22,c23,c24,c25,c26,c27,c28,c29,c30,c31,c32,c33,c34,c35,c36,c37,c38,c39,c40,c41,c42,c43,c44,c45,c46,c47,c48,c49,c50,c51,c52,c53,c54,c55,c56,c57,c58,c59,c60,c61,c62,c63,c64,c65,c66,c67,c68,c69,c70,c71,c72,c73,c74,c75,c76,c77,c78,c79,c80,c81,c82,c83,c84,c85,c86,c87,c88,c89,c90,c91,c92,c93,c94,c95,c96,c97,c98,c99,c100,c101,c102,c103,c104,c105,c106,c107,c108
# --- End of included input --- The GROUP action with label Ncenter calculates somethingC: 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=1-864:8
The GROUP action with label C calculates somethingO: 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=2-864:8
The GROUP action with label O calculates somethingN1: 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=3-864:8
The GROUP action with label N1 calculates somethingN2: 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=6-864:8
 
# Define the CV

The GROUP action with label N2 calculates somethingPAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s1
 CENTER=C
 START=Ncenter
 END=O
 MAXR=0.6
 SIGMA=0.05,0.25
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPYThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=s2
 CENTER=C
 START=N1
 END=N2
 MAXR=0.6
 SIGMA=0.05,0.125
 UP_DOWN_SYMMETRY
... PAIR_ORIENTATIONAL_ENTROPY

MANY_ANGLEThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=ma1
 CENTER=C
 START=C
 END=O
 RCUT=0.64
 NOPBC
... MANY_ANGLE

MANY_ANGLEThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=ma2
 CENTER=C
 START=N1
 END=N2
 RCUT=0.64
 NOPBC
... MANY_ANGLE

# Construct a bias potential using metadynamics

COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc  ARGthe values input to this function=s1,s2,ma1,ma2 COEFFICIENTS the coefficients of the arguments in your function=0.513,0.938,-0.129,1.00 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE

The COMBINE action with label rc calculates the following quantities:
 Quantity   
 Description  
rc.value
a linear compbinationMETADUsed to performed metadynamics on one or more collective variables. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metad
 ARGthe labels of the scalars on which the bias will act=rc   # Label of the CV
 PACEthe frequency for hill addition=2500   # Pace in the deposition of the gaussians
 HEIGHTthe heights of the Gaussian hills=18.705   # Height of the gaussians in energy units kJ/mol. This is 5 kT.
 SIGMAthe widths of the Gaussian hills=0.10   # Width of the gaussian in CV units
 FILE a file in which the list of added hills is stored=HILLS   # File where the information of the gaussians is printed
 BIASFACTORuse well tempered metadynamics and use this bias factor=50.0   # Bias factor in well tempered simulations
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=450.0   # Temperature in Kelvin. Only needed for well tempered simulations
 GRID_MINthe lower bounds for the grid=-20.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 GRID_MAXthe upper bounds for the grid=2.0
 GRID_BINthe number of bins for the grid=600
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

# Print value of the CV and bias to a file named COLVAR
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  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