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 VECTOR1two atoms that define a vector=HCOM1,COM1 AXIStwo atoms that define an axis=DUM1,DUM2 VECTOR2two atoms that define a vector=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 VECTOR1two atoms that define a vector=HCOM2,COM2 AXIStwo atoms that define an axis=DUM1,DUM2 VECTOR2two atoms that define a vector=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