Project ID: plumID:26.006
Source: PARK7_chainA_pY67_TYR_COORD_METAD_BF40/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
# protein info MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=processed_chainA.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein # whole molecule for all the backbone atoms WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2842 # dihedral angles # P2719 ZETA zeta: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=976,980,982,985 # P2719 PSI psi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=981,985,993,995 COORDINATIONCalculate coordination numbers. More details ... GROUPAFirst list of atoms=1002,1003,1005,1007,1008,1013,1015 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,5,7,10,13,14,18,19,20,22,24,28,29,30,32,34,37,39,40,41,43,45,48,51,54,57,61,62,63,65,67,70,73,76,78,79,82,85,86,87,89,91,95,96,97,99,101,104,106,110,114,115,116,118,120,122,126,130,131,132,134,136,138,142,145,149,150,151,153,155,158,160,164,168,169,170,172,174,178,179,180,182,184,187,190,193,196,200,201,202,204,207,208,209,211,213,217,218,219,221,223,226,229,230,231,232,233,234,236,238,241,244,245,246,247,248,249,251,253,256,259,260,264,265,266,268,270,273,276,277,278,280,281,282,284,286,288,290,294,295,296,298,300,302,306,310,311,312,314,316,318,322,325,329,330,331,332,335,337,340,343,344,345,347,349,351,355,359,360,361,363,365,368,369,370,371,372,373,375,377,379,383,387,388,389,391,393,396,399,400,404,405,406,408,410,413,416,419,421,422,425,428,429,430,432,434,437,440,443,445,446,449,452,453,454,456,458,462,463,464,466,469,470,471,473,475,477,481,484,488,489,490,492,494,497,500,503,506,510,511,512,514,516,518,522,526,527,528,530,532,534,536,540,541,542,544,546,548,552,556,557,558,560,562,566,567,568,570,573,574,575,577,579,582,584,588,592,593,594,596,598,602,603,604,606,609,610,611,613,615,618,621,624,627,631,632,633,635,637,640,641,642,643,644,645,646,649,651,654,657,658,659,661,663,665,669,673,674,675,677,679,682,685,686,687,690,691,692,694,696,699,701,702,703,705,707,710,712,713,714,716,718,721,724,727,729,730,733,736,737,738,740,742,745,746,747,748,749,750,752,754,756,760,764,765,766,768,770,772,776,780,781,782,784,786,788,792,795,799,800,801,803,805,808,810,811,812,813,816,818,821,824,825,826,828,830,833,834,835,836,837,838,840,842,846,847,848,850,852,855,857,858,859,861,863,866,868,872,876,877,878,880,882,885,888,889,890,891,892,893,895,897,900,901,902,903,904,905,907,909,913,914,915,917,919,922,925,928,931,935,936,937,939,941,944,947,950,953,957,958,959,961,963,966,969,970,971,972,973,974,976,979,980,981,982,985,987,990,993,994,1019,1021,1023,1026,1027,1028,1029,1030,1031,1033,1035,1037,1041,1045,1046,1047,1049,1051,1053,1057,1061,1062,1063,1065,1067,1069,1073,1077,1078,1079,1081,1083,1086,1088,1092,1096,1097,1098,1099,1102,1104,1107,1110,1111,1112,1114,1117,1118,1119,1121,1124,1125,1126,1128,1130,1133,1134,1135,1138,1139,1140,1142,1144,1147,1149,1153,1157,1158,1159,1161,1164,1165,1166,1168,1170,1174,1175,1176,1178,1180,1183,1186,1187,1188,1191,1192,1193,1195,1197,1200,1201,1202,1205,1206,1207,1209,1211,1214,1216,1220,1224,1225,1226,1228,1230,1233,1235,1236,1237,1239,1241,1244,1247,1248,1249,1250,1251,1252,1254,1256,1259,1261,1262,1263,1265,1267,1271,1272,1273,1275,1277,1281,1282,1283,1285,1287,1289,1293,1297,1298,1299,1301,1303,1306,1309,1312,1315,1319,1320,1321,1323,1325,1328,1331,1332,1333,1334,1335,1336,1338,1340,1342,1346,1349,1353,1354,1355,1357,1359,1362,1364,1368,1372,1373,1374,1376,1378,1381,1384,1387,1390,1394,1395,1396,1398,1400,1403,1406,1407,1408,1409,1410,1411,1413,1415,1418,1421,1422,1423,1426,1427,1428,1430,1432,1435,1438,1439,1440,1441,1442,1443,1445,1447,1450,1451,1452,1455,1456,1457,1459,1461,1464,1467,1470,1472,1473,1476,1479,1480,1481,1483,1485,1488,1491,1494,1497,1501,1502,1503,1505,1508,1509,1510,1512,1514,1517,1519,1523,1527,1528,1529,1531,1533,1535,1539,1542,1546,1547,1548,1550,1552,1556,1557,1558,1560,1562,1566,1567,1568,1570,1572,1574,1578,1581,1585,1586,1587,1589,1591,1594,1595,1596,1597,1599,1601,1605,1606,1607,1609,1612,1613,1614,1615,1618,1620,1623,1626,1627,1628,1630,1632,1634,1636,1640,1641,1642,1644,1646,1650,1651,1652,1654,1656,1659,1661,1665,1669,1670,1671,1673,1675,1678,1680,1684,1688,1689,1690,1692,1694,1698,1699,1700,1702,1704,1707,1708,1709,1711,1713,1715,1716,1717,1719,1721,1724,1727,1728,1729,1730,1731,1732,1734,1736,1738,1742,1745,1749,1750,1751,1753,1756,1757,1758,1760,1762,1765,1766,1768,1770,1772,1774,1776,1777,1778,1780,1783,1784,1785,1787,1789,1792,1794,1795,1796,1798,1800,1803,1806,1809,1812,1816,1817,1818,1820,1822,1824,1828,1832,1833,1834,1836,1838,1840,1842,1846,1847,1848,1850,1852,1854,1856,1860,1861,1862,1864,1866,1869,1870,1871,1873,1875,1877,1878,1879,1880,1883,1885,1888,1891,1892,1893,1895,1897,1900,1902,1906,1910,1911,1912,1914,1916,1920,1921,1922,1924,1926,1929,1932,1935,1938,1942,1943,1944,1946,1948,1951,1952,1953,1954,1955,1956,1958,1960,1963,1966,1969,1972,1976,1977,1978,1980,1982,1985,1988,1989,1993,1994,1995,1997,1999,2002,2005,2006,2010,2011,2012,2014,2016,2019,2020,2021,2024,2025,2026,2028,2031,2032,2033,2035,2038,2039,2040,2042,2044,2047,2048,2049,2051,2053,2055,2056,2057,2059,2061,2064,2065,2067,2069,2070,2072,2074,2076,2077,2078,2080,2082,2084,2086,2090,2091,2092,2094,2096,2099,2100,2102,2104,2105,2107,2109,2111,2112,2113,2115,2117,2120,2122,2123,2124,2126,2128,2131,2134,2135,2136,2137,2138,2139,2141,2143,2146,2147,2148,2151,2152,2153,2155,2157,2160,2163,2166,2168,2169,2172,2175,2176,2177,2179,2181,2183,2187,2191,2192,2193,2195,2197,2200,2203,2204,2205,2206,2207,2208,2210,2212,2215,2218,2221,2224,2228,2229,2230,2232,2234,2237,2238,2239,2240,2241,2242,2244,2247,2248,2249,2251,2253,2256,2258,2262,2266,2267,2268,2270,2272,2274,2278,2281,2285,2286,2287,2289,2291,2294,2296,2300,2304,2305,2306,2308,2310,2312,2314,2318,2319,2320,2322,2324,2327,2329,2330,2331,2333,2335,2338,2341,2344,2346,2347,2350,2353,2354,2355,2357,2360,2361,2362,2363,2366,2368,2371,2374,2375,2376,2378,2381,2382,2383,2385,2387,2389,2391,2395,2396,2397,2399,2401,2404,2406,2407,2408,2410,2412,2415,2416,2418,2420,2422,2424,2426,2427,2428,2430,2432,2435,2438,2439,2440,2441,2442,2443,2445,2447,2450,2451,2453,2455,2457,2459,2461,2462,2463,2465,2467,2471,2472,2473,2475,2477,2480,2482,2486,2490,2491,2492,2494,2496,2500,2501,2502,2504,2506,2508,2512,2515,2519,2520,2521,2523,2525,2527,2531,2535,2536,2537,2539,2541,2544,2547,2548,2549,2550,2551,2552,2554,2556,2560,2561,2562,2564,2566,2569,2571,2575,2579,2580,2581,2583,2585,2588,2589,2590,2593,2594,2595,2597,2600,2601,2602,2604,2606,2609,2612,2615,2618,2622,2623,2624,2626,2628,2631,2634,2635,2636,2637,2638,2639,2641,2643,2645,2649,2653,2654,2655,2657,2659,2663,2664,2665,2667,2669,2673,2674,2675,2677,2679,2682,2685,2686,2687,2690,2691,2692,2694,2696,2698,2702,2706,2707,2708,2710,2712,2715,2718,2721,2724,2728,2729,2730,2732,2734,2738,2739,2740,2741,2744,2746,2749,2752,2753,2754,2756,2758,2761,2763,2767,2771,2772,2773,2775,2777,2779,2783,2787,2788,2789,2791,2793,2796,2798,2802,2806,2807,2808,2810,2812,2815,2818,2821,2824,2828,2829,2830,2832,2834,2837,2838,2839,2840,2841,2842 R_0The r_0 parameter of the switching function=0.6 NOPBC ignore the periodic boundary conditions when calculating distances NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=50 LABELa label for the action so that its output can be referenced in the input to other actions=coord ... COORDINATION
# METAD METADUsed to performed metadynamics on one or more collective variables. More details ... ARGthe labels of the scalars on which the bias will act=zeta,coord PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.8 BIASFACTORuse well tempered metadynamics and use this bias factor=40 SIGMAthe widths of the Gaussian hills=0.07,2.0 GRID_MINthe lower bounds for the grid=-pi,0 GRID_MAXthe upper bounds for the grid=pi,500 FILE a file in which the list of added hills is stored=HILLS_PRO TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] LABELa label for the action so that its output can be referenced in the input to other actions=metad ... METAD
# Print out information PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=zeta,psi,coord,metad.rbias,metad.rct,metad.bias STRIDE the frequency with which the quantities of interest should be output=2500 FILEthe name of the file on which to output these quantities=COLVAR