PLUMED-NEST

Project ID: plumID:19.035
Source: plumed.dat
Originally used with PLUMED version: 2.2.3
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

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### CENTER OF MASS DEFINITIONS
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# COM of both protomers (only BB atoms)
COM1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,3,5,7,8,10,12,14,16,17,19,23,25,27,29,31,33,35,36,38,42,43,45,49,51,53,55,59,61,63,65,68,72,74,77,79,82,84,85,87,89,91,95,97,101,103,105,106,108,109,111,112,114,115,117,119,121,123,125,129,131,133,135,137,141,143,145,146,148,153,155,159,160,162,164,166,168,171,173,175,177,179,181,183,187,191,193,195,199,201,203,205,209,211,213,215,217,219,221,223,225,228,232,234,235,237,243,247,249,251,254,255,257,259,263,266,268,270,273,275,276,279,281,283,285,287,289,291,296,298,300,302,304,305,307,308,310,312,314,316,320,322,323,325,327,330,334,337,339,340,342,344,346,348,350,352,354,358,360,364,366,368,373,377,382,384,386,388,390,393,395,397,399,403,405,409,410,414,416,418,420,422,424,426,428,430,432,434,438,439,441,443,445,447,450,452,455,457,459,462,464,466,468,469,471,474,476,479,481,484,486,488,491,494,496,498,501,503,505,507,509,511,513,514,516,520,522,524,526,531,533,535,537,541,543,547,549,551,553,556,557,559,561,563,565,567,569,571,573,577,579,581,583,585,590,594,598,600,602,603,605,606,610,612,614,616,618,620,622,624,626,628,632,633,637,639,641,643,645,649,652,655,657,661,664,666,670,672
The COM action with label COM1 calculates somethingCOM2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=674,676,678,680,681,683,685,687,689,690,692,696,698,700,702,704,706,708,709,711,715,716,718,722,724,726,728,732,734,736,738,741,745,747,750,752,755,757,758,760,762,764,768,770,774,776,778,779,781,782,784,785,787,788,790,792,794,796,798,802,804,806,808,810,814,816,818,819,821,826,828,832,833,835,837,839,841,844,846,848,850,852,854,856,860,864,866,868,872,874,876,878,882,884,886,888,890,892,894,896,898,901,905,907,908,910,916,920,922,924,927,928,930,932,936,939,941,943,946,948,949,952,954,956,958,960,962,964,969,971,973,975,977,978,980,981,983,985,987,989,993,995,996,998,1000,1003,1007,1010,1012,1013,1015,1017,1019,1021,1023,1025,1027,1031,1033,1037,1039,1041,1046,1050,1055,1057,1059,1061,1063,1066,1068,1070,1072,1076,1078,1082,1083,1087,1089,1091,1093,1095,1097,1099,1101,1103,1105,1107,1111,1112,1114,1116,1118,1120,1123,1125,1128,1130,1132,1135,1137,1139,1141,1142,1144,1147,1149,1152,1154,1157,1159,1161,1164,1167,1169,1171,1174,1176,1178,1180,1182,1184,1186,1187,1189,1193,1195,1197,1199,1204,1206,1208,1210,1214,1216,1220,1222,1224,1226,1229,1230,1232,1234,1236,1238,1240,1242,1244,1246,1250,1252,1254,1256,1258,1263,1267,1271,1273,1275,1276,1278,1279,1283,1285,1287,1289,1291,1293,1295,1297,1299,1301,1305,1306,1310,1312,1314,1316,1318,1322,1325,1328,1330,1334,1337,1339,1343,1345
# COM of Helix 1 for both protomers (only BB atoms)
The COM action with label COM2 calculates somethingHCOM1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,3,5,7,8,10,12,14,16,17,19,23,25,27,29,31,33,35,36,38,42,43,45,49,51,53,55,59,61,63,65
The COM action with label HCOM1 calculates somethingHCOM2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=674,676,678,680,681,683,685,687,689,690,692,696,698,700,702,704,706,708,709,711,715,716,718,722,724,726,728,732,734,736,738

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### DEFINITION DUMMY ATOMS
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The COM action with label HCOM2 calculates somethingDUM1: 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=20424
The GROUP action with label DUM1 calculates somethingDUM2: 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=20425
The GROUP action with label DUM2 calculates somethingZAXE: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=DUM1,DUM2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label

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### DEFINITION OF DISTANCE AND ANGLES
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The DISTANCE action with label ZAXE calculates the following quantities:
 Quantity   
 Description  
ZAXE.x
the x-component of the vector connecting the two atoms
ZAXE.y
the y-component of the vector connecting the two atoms
ZAXE.z
the z-component of the vector connecting the two atoms
ZAXE.value
the DISTANCE between this pair of atomsDIST: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM1,COM2 
The DISTANCE action with label DIST calculates the following quantities:
 Quantity   
 Description  
DIST.value
the DISTANCE between this pair of atomsANG1: TORSIONCalculate one or multiple torsional angles. More details VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=HCOM1,COM1 AXIStwo atoms that define an axis=DUM1,DUM2 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=COM2,COM1
The TORSION action with label ANG1 calculates the following quantities:
 Quantity   
 Description  
ANG1.value
the TORSION involving these atomsANG2: TORSIONCalculate one or multiple torsional angles. More details VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=HCOM2,COM2 AXIStwo atoms that define an axis=DUM1,DUM2 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=COM1,COM2

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### DEFINITION OF UMBRELLA SAMPLING RESTRAINTS
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The TORSION action with label ANG2 calculates the following quantities:
 Quantity   
 Description  
ANG2.value
the TORSION involving these atomsRESTUS: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=DIST,ANG1,ANG2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=250.0,100.0,100.0 ATthe position of the restraint=4.400,-1.581,-1.284

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### PRINTING OUT
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The RESTRAINT action with label RESTUS calculates the following quantities:
 Quantity   
 Description  
RESTUS.bias
the instantaneous value of the bias potential
RESTUS.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ZAXE.x,ZAXE.y,ZAXE.z STRIDE the frequency with which the quantities of interest should be output=25000 FILEthe name of the file on which to output these quantities=ZAXE.dat
The PRINT action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=DIST,ANG1,ANG2       STRIDE the frequency with which the quantities of interest should be output=25000 FILEthe name of the file on which to output these quantities=COLVALS.dat
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=RESTUS.bias          STRIDE the frequency with which the quantities of interest should be output=25000 FILEthe name of the file on which to output these quantities=EBIAS.dat