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BibTeX entry
@Article{Swanson:1995:PAP,
author = "Eric Swanson and Terry P. Lybrand",
title = "{PVM-AMBER}: a parallel implementation of the {AMBER}
molecular mechanics package for workstation clusters",
journal = j-J-COMPUT-CHEM,
volume = "16",
number = "9",
pages = "1131--1140",
month = sep,
year = "1995",
CODEN = "JCCHDD",
DOI = "https://doi.org/10.1002/jcc.540160907",
ISSN = "0192-8651 (print), 1096-987X (electronic)",
ISSN-L = "0192-8651",
bibdate = "Thu Nov 29 14:54:31 MST 2012",
bibsource = "http://www.interscience.wiley.com/jpages/0192-8651;
http://www.math.utah.edu/pub/tex/bib/jcomputchem1990.bib;
http://www.math.utah.edu/pub/tex/bib/pvm.bib",
acknowledgement = ack-nhfb,
affiliation = "Center for Bioeng., Washington Univ., Seattle, WA,
USA",
classification = "A3620C (Macromolecular conformation (statistics and
dynamics)); A8710 (General, theoretical, and
mathematical biophysics); A8715D (Physical chemistry of
biomolecular solutions; A8715H (Biomolecular dynamics,
molecular probes, molecular pattern recognition);
C6150N (Distributed systems software); C6185
(Simulation techniques); C7320 (Physics and chemistry
computing); C7330 (Biology and medical computing);
condensed states)",
corpsource = "Center for Bioeng., Washington Univ., Seattle, WA,
USA",
fjournal = "Journal of Computational Chemistry",
journal-URL = "http://www.interscience.wiley.com/jpages/0192-8651",
keywords = "AMBER molecular mechanics package parallel version;
biology computing; biomolecular simulation;
Biomolecular simulation problems; Computational
speedup; computational speedup; computations; Data
exchange; data exchange; digital simulation;
efficiency; Ethernet; FDDI; FDDI connections; free
energy; Free-energy perturbation computations;
free-energy perturbation computations; intermolecular
mechanics; Lipid bilayer systems; lipid bilayer
systems; lipid bilayers; local area; molecular
biophysics; molecular dynamics; Molecular dynamics
computations; molecular dynamics method; networks;
Nonbonded energies; nonbonded energies; Nonbonded
forces; nonbonded forces; Nonbonded pair list
generation; nonbonded pair list generation; packages;
parallel; Parallel efficiency; parallel processing;
peptide; perturbation theory; problems; Processor
synchronization; processor synchronization; Protein;
protein; proteins; PVM message-passing software;
PVM-AMBER; Silicon Graphics; software; solvated;
Solvated peptide; Test simulations; test simulations;
Unix; Unix workstations; Workstation clusters;
workstation clusters; workstations",
onlinedate = "7 Sep 2004",
thesaurus = "Biology computing; Digital simulation; FDDI; Free
energy; Intermolecular mechanics; Lipid bilayers; Local
area networks; Molecular biophysics; Molecular dynamics
method; Parallel processing; Perturbation theory;
Proteins; Software packages; Unix; Workstations",
treatment = "P Practical",
}
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- AMBER,
14(3)312,
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18(9)1136
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12(7)868,
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13(1)1,
14(3)349,
14(5)510,
14(6)741,
15(11)1228,
16(3)273,
16(7)817,
16(8)1038,
17(8)962,
17(8)970,
18(1)115,
19(3)319,
19(7)797,
19(9)1110,
20(7)688
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16(2)235,
16(11)1420,
20(11)1153
- biomolecular,
11(3)374,
13(9)1151,
14(7)867,
15(5)532,
20(11)1165,
20(11)1177,
20(13)1329
- biophysics,
16(11)1420
- C7320,
15(9)937,
16(11)1420
- chemistry,
0(0)viii--224,
0(0)ix--233,
0(0)xiv--247,
0(0)xx--349,
11(2)181,
11(3)410,
11(8)899,
12(1)139,
12(5)635,
13(2)254,
13(5)614,
15(9)937,
16(1)37,
16(11)1420,
16(11)1445,
17(1)109,
17(1)124,
17(13)1571,
18(10)1327,
18(16)2075,
19(2)139,
19(9)1053,
19(9)1101,
19(13)1553,
36(30)2270
- cluster,
11(1)67,
12(1)52,
12(9)1097,
13(7)867,
14(6)667,
14(6)680,
14(10)1142,
14(11)1326,
14(12)1423,
14(12)1468,
14(12)1534,
15(6)633,
15(8)899,
16(11)1315,
17(8)1056,
18(4)562,
18(5)702,
18(9)1233,
18(10)1295,
18(14)1695,
18(16)2040,
19(1)60,
19(2)203,
20(2)253,
20(7)679,
20(11)1145,
20(16)1752
- computation,
11(1)112,
11(3)396,
12(2)231,
12(5)611,
12(6)664,
12(7)779,
12(8)970,
12(8)981,
12(10)1260,
13(6)675,
14(7)769,
14(8)944,
14(11)1396,
15(3)269,
15(7)752,
15(7)782,
15(10)1127,
15(12)1393,
16(4)395,
16(7)817,
16(7)856,
17(2)148,
17(8)976,
17(14)1612,
18(1)20,
18(2)159,
18(4)569,
18(6)816,
19(7)797,
19(9)1110,
20(4)383,
20(4)396,
20(8)781
- computational,
0(0)viii--224,
0(0)xiv--247,
0(0)xx--349,
0(0)278,
0(0)331,
11(2)181,
11(2)242,
11(3)410,
12(5)635,
12(7)784,
13(2)254,
13(5)614,
13(6)792,
14(1)75,
14(7)809,
14(8)961,
14(11)1272,
15(2)241,
15(9)937,
15(10)1163,
17(1)109,
17(1)124,
17(2)204,
17(3)313,
17(5)616,
17(10)1245,
17(13)1571,
18(1)70,
18(10)1327,
19(8)902,
19(12)1353,
20(13)1371,
20(14)1587,
20(15)1634,
36(30)2270
- computing,
11(5)603,
12(3)391,
12(7)792,
12(9)1077,
12(10)1223,
15(9)937,
16(11)1420,
17(7)864,
17(14)1633,
19(8)923
- condensed,
15(8)838
- conformation,
11(2)265,
11(5)644,
12(1)113,
12(3)402,
12(4)505,
12(7)829,
12(9)1065,
13(3)351,
13(5)579,
14(1)114,
14(4)438,
14(6)715,
14(7)790,
14(8)899,
14(11)1333,
14(11)1385,
15(0)x--541,
15(2)132,
15(2)155,
15(3)300,
15(5)488,
15(6)627,
15(8)899,
15(9)937,
15(10)1091,
15(10)1176,
16(2)243,
17(14)1667,
18(3)323,
18(10)1295,
18(12)1450,
18(16)2086,
19(2)123,
19(12)1337,
20(6)636,
20(9)947,
20(9)971,
20(13)1329
- connection,
19(4)418
- data,
0(0)viii--224,
0(0)xiv--247,
0(0)xx--349,
0(0)278,
11(1)45,
13(6)749,
14(2)226,
14(2)246,
14(5)579,
14(8)899,
14(12)1429,
15(1)44,
15(2)155,
15(2)190,
15(12)1429,
16(4)414,
16(6)715,
16(11)1394,
17(4)409,
17(5)616,
18(2)240,
18(3)313,
18(4)478,
18(7)849,
19(7)695,
19(10)1146,
20(5)546,
20(11)1177,
20(13)1354,
20(15)1634,
20(16)1760
- distributed,
12(8)913,
12(10)1187,
14(12)1429,
15(9)937,
16(1)91,
16(4)395,
16(5)628,
16(9)1141,
18(2)159,
18(4)552
- efficiency,
11(9)1021,
14(8)977,
14(11)1272,
14(12)1468,
17(8)1068,
18(2)240,
19(14)1632,
20(8)786,
20(15)1659
- energy, Free-,
16(11)1420
- energy, free-,
13(8)1011,
16(3)311,
16(11)1339,
16(11)1420,
17(10)1269
- exchange,
12(7)803,
14(10)1149,
18(14)1792,
19(4)418,
19(16)1816,
20(1)2,
20(13)1391
- force,
11(3)351,
11(3)401,
11(5)560,
11(5)623,
11(5)654,
11(6)734,
11(7)819,
11(7)848,
11(10)1125,
12(1)78,
12(1)91,
12(2)186,
12(3)385,
12(4)469,
12(5)575,
12(6)664,
12(6)731,
12(6)761,
12(7)844,
12(8)934,
12(10)1232,
13(3)257,
13(5)585,
13(7)888,
13(9)1098,
13(9)1142,
14(1)45,
14(3)263,
14(3)353,
14(6)728,
14(6)751,
14(9)1066,
14(11)1281,
15(2)162,
15(3)251,
15(4)405,
15(4)455,
15(7)667,
15(7)684,
15(7)752,
15(9)1019,
15(11)1254,
15(11)1291,
16(1)56,
16(2)188,
16(5)527,
16(5)595,
16(5)610,
16(7)883,
16(8)923,
16(8)937,
16(8)973,
16(9)1120,
17(4)450,
17(5)490,
17(5)520,
17(5)553,
17(5)587,
17(5)616,
17(5)642,
17(8)1068,
17(9)1112,
17(12)1406,
17(13)1541,
18(2)211,
18(2)221,
18(3)351,
18(4)449,
18(4)533,
18(7)849,
18(7)874,
18(8)1043,
18(11)1371,
18(13)1656,
18(13)1664,
18(14)1750,
18(16)1955,
18(16)2050,
18(16)2093,
19(3)259,
19(4)430,
19(5)535,
19(7)754,
19(7)769,
19(9)1001,
19(10)1187,
19(13)1515,
20(4)455,
20(5)531,
20(7)704,
20(7)730,
20(8)799,
20(10)1009,
20(11)1165,
20(11)1177
- free,
11(1)76,
11(4)511,
11(8)994,
12(1)42,
12(2)271,
12(7)899,
12(10)1165,
12(10)1232,
13(3)362,
13(4)429,
13(5)541,
13(5)651,
13(5)667,
13(9)1057,
14(5)620,
14(10)1240,
14(12)1498,
15(1)105,
15(2)149,
15(3)333,
15(3)351,
15(7)704,
15(11)1241,
16(3)370,
16(11)1420,
16(12)1513,
17(2)148,
17(3)273,
17(9)1112,
17(9)1156,
17(14)1587,
17(15)1726,
18(4)449,
18(7)902,
18(10)1320,
19(7)769,
19(8)977,
19(11)1229,
19(11)1278,
19(13)1494,
19(14)1639,
19(15)1724,
19(15)1736,
19(16)1853,
20(5)499,
20(8)749,
20(8)877,
20(10)1018,
20(10)1028,
20(15)1604,
20(15)1644
- free-energy,
13(8)1011,
16(3)311,
16(11)1339,
16(11)1420,
17(10)1269
- general,
11(1)105,
11(8)943,
12(1)71,
12(2)209,
12(2)237,
12(8)981,
12(8)1014,
12(9)1089,
13(7)888,
13(9)1089,
13(9)1119,
13(10)1171,
13(10)1262,
14(11)1347,
15(1)90,
15(9)937,
18(1)139,
18(11)1365,
18(12)1513,
19(3)368,
19(6)593,
19(10)1167,
19(13)1431,
20(3)305
- generation,
0(0)278,
11(2)223,
11(5)589,
11(7)829,
12(10)1252,
13(1)33,
14(2)246,
14(5)603,
16(11)1394,
18(13)1570,
19(1)1,
19(11)1268,
20(5)483,
20(8)799,
20(16)1693
- implementation,
11(8)972,
12(1)71,
12(4)487,
12(5)560,
12(8)943,
13(2)160,
14(7)818,
15(1)44,
15(8)814,
15(12)1393,
16(1)37,
16(1)91,
16(2)226,
16(9)1153,
16(10)1301,
16(11)1420,
16(11)1445,
17(4)476,
17(10)1217,
18(5)694,
19(4)418,
19(6)658,
19(9)1101,
20(6)604,
20(14)1559
- intermolecular,
11(10)1217,
12(7)811,
12(8)1008,
14(4)401,
15(9)1013,
15(11)1187,
16(1)131,
16(4)441,
16(7)883,
17(5)520,
19(16)1816,
20(2)274
- lipid,
12(8)1033,
13(5)622,
14(9)1066,
15(2)208,
16(2)235,
16(11)1420,
20(11)1153
- list,
19(7)685
- local,
11(1)58,
11(6)694,
11(9)1087,
14(6)736,
15(3)269,
16(12)1459,
19(2)195,
19(11)1241,
20(11)1091
- macromolecular,
12(2)175,
13(6)730,
15(7)667,
16(10)1238,
16(11)1351,
16(11)1420,
17(3)326,
18(4)569
- mathematical,
0(0)xvii--493,
11(2)266,
12(3)385,
15(9)937,
18(15)1903
- mechanics,
11(3)326,
11(4)440,
11(6)734,
11(7)848,
11(7)868,
11(8)952,
11(9)1061,
11(9)1087,
12(1)78,
12(2)200,
12(3)310,
12(3)385,
12(4)427,
12(5)575,
12(5)620,
12(7)839,
12(7)872,
12(7)880,
12(8)943,
12(8)994,
12(10)1232,
13(1)57,
13(4)408,
13(4)525,
13(5)541,
13(5)633,
13(7)851,
13(8)971,
13(9)1125,
13(9)1138,
13(9)1142,
14(3)353,
14(4)379,
14(4)455,
14(6)655,
14(7)755,
14(8)881,
14(8)977,
15(2)190,
15(3)283,
15(3)333,
15(8)866,
15(10)1105,
15(11)1228,
15(11)1254,
15(12)1321,
15(12)1446,
16(1)1,
16(5)620,
16(7)856,
16(9)1170,
16(10)1250,
17(1)19,
17(2)156,
17(4)396,
17(4)429,
17(5)669,
17(5)695,
17(5)730,
17(5)747,
17(8)1013,
17(9)1132,
17(11)1328,
17(12)1395,
17(12)1481,
17(13)1564,
18(2)221,
18(2)254,
18(4)449,
18(5)712,
18(8)1056,
18(9)1211,
18(11)1371,
18(12)1496,
18(12)1523,
18(13)1632,
18(14)1804,
18(15)1827,
19(1)71,
19(5)512,
19(7)754,
19(10)1146,
19(10)1167,
19(12)1370,
19(12)1387,
19(12)1402,
20(6)604,
20(10)1028,
20(10)1067,
20(13)1379,
20(13)1401,
20(15)1618
- network,
14(7)818,
15(6)633,
15(9)937,
16(8)923,
17(4)469,
17(14)1667,
18(11)1407,
18(12)1513,
20(4)455,
20(10)1060
- nonbonded,
12(9)1125,
14(1)19,
14(3)295,
16(9)1120
- package,
16(11)1420,
20(4)412,
20(8)799
- pair,
11(7)819,
13(7)901,
14(6)685,
15(9)981,
16(6)777,
16(11)1428,
19(7)685,
19(12)1325,
20(5)511
- parallel,
11(3)314,
11(10)1151,
12(7)779,
12(10)1270,
13(2)155,
13(2)160,
13(4)533,
13(9)1098,
14(4)445,
14(8)977,
14(10)1142,
14(12)1429,
15(1)44,
15(2)144,
15(3)351,
15(9)937,
16(1)91,
16(2)226,
16(4)395,
16(9)1141,
16(10)1291,
16(10)1301,
16(11)1420,
17(2)250,
17(3)326,
17(4)469,
17(8)992,
17(10)1217,
17(15)1712,
18(2)159,
18(3)430,
18(4)501,
18(4)552,
18(6)816,
19(6)658,
19(7)685,
19(9)1017,
19(9)1030,
19(9)1053,
19(9)1101,
19(11)1215,
19(15)1716,
19(15)1746,
20(2)185,
20(14)1559
- pattern,
11(3)374,
14(10)1164,
18(15)1875
- peptide,
11(4)468,
11(4)487,
11(9)1087,
13(4)429,
13(6)704,
14(4)471,
14(6)715,
14(8)970,
14(11)1333,
15(1)23,
15(6)662,
16(8)984,
16(11)1434,
17(4)418,
17(7)790,
17(7)821,
17(13)1549,
18(2)240,
18(3)323,
18(12)1450,
18(14)1720,
18(15)1893,
18(16)1971,
19(4)430,
19(11)1294,
19(15)1724,
20(3)354,
20(6)636,
20(9)947,
20(9)971,
20(12)1254,
20(13)1354,
20(15)1659
- perturbation,
11(8)994,
11(10)1217,
13(3)362,
13(5)667,
14(1)13,
15(3)351,
15(11)1241,
16(3)311,
16(10)1301,
16(11)1420,
16(12)1513,
17(9)1112,
18(1)20,
19(8)977,
20(2)274,
20(5)499,
20(10)1018
- physical,
11(4)493
- physics,
0(0)xix--393,
15(9)937,
16(11)1420
- probe,
19(6)673
- problem,
12(1)52,
12(2)237,
12(6)746,
12(10)1243,
13(10)1199,
14(4)452,
14(5)549,
14(11)1333,
15(1)105,
15(6)627,
15(8)858,
16(6)729,
16(12)1449,
17(2)133,
17(8)1002,
17(9)1085,
17(13)1497,
18(7)920,
18(15)1943,
20(14)1455
- processing,
0(0)viii--224,
0(0)xiv--247,
0(0)xx--349,
0(0)278,
11(3)314,
13(1)12,
13(10)1246,
14(8)977
- processor,
13(4)533,
13(9)1098,
16(9)1120,
17(15)1712,
20(2)185
- protein,
11(1)121,
11(3)314,
11(7)805,
11(9)1087,
11(10)1169,
12(2)180,
12(2)186,
12(3)359,
12(3)410,
12(5)635,
12(6)717,
12(6)746,
12(7)899,
13(3)329,
13(4)443,
13(4)533,
13(7)793,
13(9)1098,
14(1)19,
14(2)161,
14(3)295,
14(5)510,
14(7)790,
14(9)1007,
14(10)1194,
15(3)300,
15(5)488,
15(7)684,
15(8)820,
15(11)1217,
15(11)1278,
16(3)328,
16(4)478,
16(7)791,
16(11)1357,
16(11)1405,
16(12)1543,
17(2)226,
17(4)469,
17(7)790,
17(7)878,
17(8)1002,
17(10)1217,
17(10)1229,
17(12)1453,
17(13)1549,
17(14)1633,
17(16)1783,
18(1)80,
18(2)169,
18(7)849,
18(7)920,
18(12)1546,
18(14)1720,
18(15)1893,
19(5)548,
19(11)1229,
19(13)1534,
20(3)354,
20(4)412,
20(7)713,
20(8)819,
20(9)983,
20(10)1049,
20(14)1455,
20(15)1634
- recognition,
11(3)374,
18(15)1875
- silicon,
12(2)254,
12(4)417,
12(4)446,
14(12)1423,
15(6)644,
17(3)306,
18(10)1253
- software,
11(4)440,
15(9)937,
20(4)412
- solution,
11(2)194,
11(3)374,
12(2)237,
12(7)909,
13(1)17,
13(2)135,
13(2)199,
13(4)429,
13(4)468,
13(5)570,
14(1)105,
14(3)353,
14(4)452,
14(6)629,
14(6)685,
14(12)1417,
15(1)61,
15(7)704,
15(11)1228,
15(11)1311,
16(3)337,
16(5)534,
17(2)148,
17(2)185,
17(3)350,
17(11)1328,
17(11)1344,
17(13)1497,
17(15)1685,
18(3)343,
18(8)1061,
18(8)1072,
18(12)1496,
18(13)1591,
19(2)144,
19(4)404,
19(8)820,
19(8)893,
19(15)1724,
20(3)301,
20(5)546,
20(7)665,
20(9)928,
20(11)1186,
20(13)1401
- solvated,
13(6)675,
15(8)847,
20(10)1039
- speedup,
15(3)351
- state,
12(1)119,
12(7)891,
13(3)275,
13(5)651,
13(7)901,
13(8)944,
13(8)979,
14(2)186,
14(3)253,
14(3)263,
14(5)566,
15(1)54,
15(2)144,
15(3)346,
15(8)893,
16(4)441,
16(9)1170,
17(1)42,
17(1)49,
17(7)888,
17(8)954,
17(9)1108,
17(14)1633,
18(2)260,
19(2)129,
19(10)1130,
20(9)897,
20(11)1112,
20(11)1130
- statistics,
16(3)285,
17(2)226
- system,
0(0)xvii--493,
11(1)112,
11(2)194,
11(2)266,
11(4)440,
11(5)545,
11(5)576,
11(6)754,
11(7)805,
12(3)369,
12(5)565,
12(5)611,
12(6)751,
12(7)899,
13(4)468,
13(4)525,
13(5)570,
13(7)830,
14(6)680,
14(6)728,
14(8)895,
14(8)944,
14(9)1027,
14(10)1136,
14(10)1149,
14(11)1272,
14(11)1347,
14(12)1446,
15(3)269,
15(5)524,
15(8)847,
15(10)1113,
15(10)1121,
15(10)1163,
15(11)1217,
16(3)311,
16(4)445,
16(6)758,
16(6)768,
16(7)898,
16(8)984,
16(10)1238,
16(12)1522,
16(12)1543,
16(12)1554,
17(2)204,
17(3)326,
17(8)940,
17(8)954,
17(11)1287,
17(13)1497,
18(1)70,
18(1)115,
18(3)381,
18(4)463,
18(4)501,
18(9)1124,
18(12)1513,
18(13)1570,
18(15)1848,
18(15)1903,
19(16)1887,
20(5)531,
20(8)786,
20(8)857,
20(10)989,
20(12)1274
- technique,
11(1)112,
11(4)411,
11(4)468,
11(5)576,
12(5)565,
12(5)611,
13(1)41,
13(2)214,
14(6)673,
14(8)977,
14(9)1085,
14(10)1212,
15(1)23,
15(7)782,
16(3)370,
16(8)923,
17(10)1269,
17(11)1328,
18(2)169,
18(4)463,
18(4)478,
18(16)2040,
19(13)1553,
20(16)1731
- test,
12(1)17,
12(6)731,
13(1)33,
14(1)37,
14(12)1454,
15(10)1121,
16(3)263,
16(8)1027,
16(10)1238,
17(8)919,
17(12)1387,
18(2)211,
18(12)1534,
20(14)1468,
36(30)2270
- theoretical,
11(3)269,
11(3)291,
11(4)524,
11(7)896,
11(9)1017,
11(10)1119,
12(1)135,
12(7)862,
12(9)1134,
12(10)1211,
13(6)681,
13(6)722,
13(7)821,
13(8)919,
13(8)935,
13(9)1047,
13(10)1184,
14(4)471,
14(4)478,
14(5)587,
14(6)699,
14(8)913,
14(12)1545,
14(12)1575,
15(5)479,
15(10)1176,
16(4)465,
16(6)659,
17(2)133,
17(3)289,
17(7)835,
17(10)1245,
17(13)1520,
17(16)1804,
18(1)56,
18(1)108,
18(7)902,
18(13)1647,
18(16)2012,
18(16)2075,
19(2)113,
19(2)240,
19(3)277,
19(8)912,
19(9)989,
19(12)1325,
19(14)1584,
19(15)1675,
19(16)1795,
19(16)1816,
19(16)1826,
20(12)1254,
20(13)1412
- theory,
0(0)278,
0(0)331,
2(0)xiii--1462-i,
11(2)266,
11(10)1217,
12(5)560,
12(7)803,
12(9)1134,
13(1)70,
13(6)792,
13(7)901,
14(5)549,
14(6)728,
15(1)90,
15(8)858,
15(9)937,
15(12)1437,
16(3)378,
16(8)984,
16(10)1301,
16(11)1315,
16(11)1420,
16(12)1468,
16(12)1483,
17(7)757,
17(7)767,
17(7)841,
18(1)20,
18(2)260,
18(6)775,
18(10)1320,
18(10)1328,
18(15)1943,
19(2)123,
19(2)154,
19(2)250,
19(6)575,
19(6)593,
19(6)610,
19(6)628,
19(9)989,
19(11)1300,
19(12)1421,
19(13)1553,
19(14)1596,
19(15)1724,
20(1)1,
20(1)12,
20(1)63,
20(1)106,
20(1)114,
20(1)129,
20(1)155,
20(2)274,
20(12)1299,
20(13)1343
- version,
0(0)331,
13(8)952,
18(5)694,
20(1)155
- workstation,
14(7)818,
14(8)907,
14(10)1142,
15(9)937,
16(11)1420