PLUMED-NEST

Project ID: plumID:26.006
Source: PARK7_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
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=1-2839

# 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
The TORSION action with label zeta calculates the following quantities:
 Quantity   
 Description  
zeta.value
the TORSION involving these atomspsi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=981,985,993,995

The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomsCOORDINATIONCalculate coordination numbers. More details ...
GROUPAFirst list of atoms=1002,1003,1005,1007,1008,1010,1012
GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1,5,7,10,13,14,18,19,20,22,24,28,29,30,32,34,37,39,40,41,43,45,48,51,54,57,61,62,63,65,67,70,73,76,78,79,82,85,86,87,89,91,95,96,97,99,101,104,106,110,114,115,116,118,120,122,126,130,131,132,134,136,138,142,145,149,150,151,153,155,158,160,164,168,169,170,172,174,178,179,180,182,184,187,190,193,196,200,201,202,204,207,208,209,211,213,217,218,219,221,223,226,229,230,231,232,233,234,236,238,241,244,245,246,247,248,249,251,253,256,259,260,264,265,266,268,270,273,276,277,278,280,281,282,284,286,288,290,294,295,296,298,300,302,306,310,311,312,314,316,318,322,325,329,330,331,332,335,337,340,343,344,345,347,349,351,355,359,360,361,363,365,368,369,370,371,372,373,375,377,379,383,387,388,389,391,393,396,399,400,404,405,406,408,410,413,416,419,421,422,425,428,429,430,432,434,437,440,443,445,446,449,452,453,454,456,458,462,463,464,466,469,470,471,473,475,477,481,484,488,489,490,492,494,497,500,503,506,510,511,512,514,516,518,522,526,527,528,530,532,534,536,540,541,542,544,546,548,552,556,557,558,560,562,566,567,568,570,573,574,575,577,579,582,584,588,592,593,594,596,598,602,603,604,606,609,610,611,613,615,618,621,624,627,631,632,633,635,637,640,641,642,643,644,645,646,649,651,654,657,658,659,661,663,665,669,673,674,675,677,679,682,685,686,687,690,691,692,694,696,699,701,702,703,705,707,710,712,713,714,716,718,721,724,727,729,730,733,736,737,738,740,742,745,746,747,748,749,750,752,754,756,760,764,765,766,768,770,772,776,780,781,782,784,786,788,792,795,799,800,801,803,805,808,810,811,812,813,816,818,821,824,825,826,828,830,833,834,835,836,837,838,840,842,846,847,848,850,852,855,857,858,859,861,863,866,868,872,876,877,878,880,882,885,888,889,890,891,892,893,895,897,900,901,902,903,904,905,907,909,913,914,915,917,919,922,925,928,931,935,936,937,939,941,944,947,950,953,957,958,959,961,963,966,969,970,971,972,973,974,976,979,980,981,982,985,987,990,993,994,1016,1018,1020,1023,1024,1025,1026,1027,1028,1030,1032,1034,1038,1042,1043,1044,1046,1048,1050,1054,1058,1059,1060,1062,1064,1066,1070,1074,1075,1076,1078,1080,1083,1085,1089,1093,1094,1095,1096,1099,1101,1104,1107,1108,1109,1111,1114,1115,1116,1118,1121,1122,1123,1125,1127,1130,1131,1132,1135,1136,1137,1139,1141,1144,1146,1150,1154,1155,1156,1158,1161,1162,1163,1165,1167,1171,1172,1173,1175,1177,1180,1183,1184,1185,1188,1189,1190,1192,1194,1197,1198,1199,1202,1203,1204,1206,1208,1211,1213,1217,1221,1222,1223,1225,1227,1230,1232,1233,1234,1236,1238,1241,1244,1245,1246,1247,1248,1249,1251,1253,1256,1258,1259,1260,1262,1264,1268,1269,1270,1272,1274,1278,1279,1280,1282,1284,1286,1290,1294,1295,1296,1298,1300,1303,1306,1309,1312,1316,1317,1318,1320,1322,1325,1328,1329,1330,1331,1332,1333,1335,1337,1339,1343,1346,1350,1351,1352,1354,1356,1359,1361,1365,1369,1370,1371,1373,1375,1378,1381,1384,1387,1391,1392,1393,1395,1397,1400,1403,1404,1405,1406,1407,1408,1410,1412,1415,1418,1419,1420,1423,1424,1425,1427,1429,1432,1435,1436,1437,1438,1439,1440,1442,1444,1447,1448,1449,1452,1453,1454,1456,1458,1461,1464,1467,1469,1470,1473,1476,1477,1478,1480,1482,1485,1488,1491,1494,1498,1499,1500,1502,1505,1506,1507,1509,1511,1514,1516,1520,1524,1525,1526,1528,1530,1532,1536,1539,1543,1544,1545,1547,1549,1553,1554,1555,1557,1559,1563,1564,1565,1567,1569,1571,1575,1578,1582,1583,1584,1586,1588,1591,1592,1593,1594,1596,1598,1602,1603,1604,1606,1609,1610,1611,1612,1615,1617,1620,1623,1624,1625,1627,1629,1631,1633,1637,1638,1639,1641,1643,1647,1648,1649,1651,1653,1656,1658,1662,1666,1667,1668,1670,1672,1675,1677,1681,1685,1686,1687,1689,1691,1695,1696,1697,1699,1701,1704,1705,1706,1708,1710,1712,1713,1714,1716,1718,1721,1724,1725,1726,1727,1728,1729,1731,1733,1735,1739,1742,1746,1747,1748,1750,1753,1754,1755,1757,1759,1762,1763,1765,1767,1769,1771,1773,1774,1775,1777,1780,1781,1782,1784,1786,1789,1791,1792,1793,1795,1797,1800,1803,1806,1809,1813,1814,1815,1817,1819,1821,1825,1829,1830,1831,1833,1835,1837,1839,1843,1844,1845,1847,1849,1851,1853,1857,1858,1859,1861,1863,1866,1867,1868,1870,1872,1874,1875,1876,1877,1880,1882,1885,1888,1889,1890,1892,1894,1897,1899,1903,1907,1908,1909,1911,1913,1917,1918,1919,1921,1923,1926,1929,1932,1935,1939,1940,1941,1943,1945,1948,1949,1950,1951,1952,1953,1955,1957,1960,1963,1966,1969,1973,1974,1975,1977,1979,1982,1985,1986,1990,1991,1992,1994,1996,1999,2002,2003,2007,2008,2009,2011,2013,2016,2017,2018,2021,2022,2023,2025,2028,2029,2030,2032,2035,2036,2037,2039,2041,2044,2045,2046,2048,2050,2052,2053,2054,2056,2058,2061,2062,2064,2066,2067,2069,2071,2073,2074,2075,2077,2079,2081,2083,2087,2088,2089,2091,2093,2096,2097,2099,2101,2102,2104,2106,2108,2109,2110,2112,2114,2117,2119,2120,2121,2123,2125,2128,2131,2132,2133,2134,2135,2136,2138,2140,2143,2144,2145,2148,2149,2150,2152,2154,2157,2160,2163,2165,2166,2169,2172,2173,2174,2176,2178,2180,2184,2188,2189,2190,2192,2194,2197,2200,2201,2202,2203,2204,2205,2207,2209,2212,2215,2218,2221,2225,2226,2227,2229,2231,2234,2235,2236,2237,2238,2239,2241,2244,2245,2246,2248,2250,2253,2255,2259,2263,2264,2265,2267,2269,2271,2275,2278,2282,2283,2284,2286,2288,2291,2293,2297,2301,2302,2303,2305,2307,2309,2311,2315,2316,2317,2319,2321,2324,2326,2327,2328,2330,2332,2335,2338,2341,2343,2344,2347,2350,2351,2352,2354,2357,2358,2359,2360,2363,2365,2368,2371,2372,2373,2375,2378,2379,2380,2382,2384,2386,2388,2392,2393,2394,2396,2398,2401,2403,2404,2405,2407,2409,2412,2413,2415,2417,2419,2421,2423,2424,2425,2427,2429,2432,2435,2436,2437,2438,2439,2440,2442,2444,2447,2448,2450,2452,2454,2456,2458,2459,2460,2462,2464,2468,2469,2470,2472,2474,2477,2479,2483,2487,2488,2489,2491,2493,2497,2498,2499,2501,2503,2505,2509,2512,2516,2517,2518,2520,2522,2524,2528,2532,2533,2534,2536,2538,2541,2544,2545,2546,2547,2548,2549,2551,2553,2557,2558,2559,2561,2563,2566,2568,2572,2576,2577,2578,2580,2582,2585,2586,2587,2590,2591,2592,2594,2597,2598,2599,2601,2603,2606,2609,2612,2615,2619,2620,2621,2623,2625,2628,2631,2632,2633,2634,2635,2636,2638,2640,2642,2646,2650,2651,2652,2654,2656,2660,2661,2662,2664,2666,2670,2671,2672,2674,2676,2679,2682,2683,2684,2687,2688,2689,2691,2693,2695,2699,2703,2704,2705,2707,2709,2712,2715,2718,2721,2725,2726,2727,2729,2731,2735,2736,2737,2738,2741,2743,2746,2749,2750,2751,2753,2755,2758,2760,2764,2768,2769,2770,2772,2774,2776,2780,2784,2785,2786,2788,2790,2793,2795,2799,2803,2804,2805,2807,2809,2812,2815,2818,2821,2825,2826,2827,2829,2831,2834,2835,2836,2837,2838,2839
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
The COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.value
the value of the coordinationMETADUsed 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
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 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