PLUMED-NEST

Project ID: plumID:24.021
Source: molecular-dynamics/ion-pairing/caco3-batches-large/3/Analysis/plumed.dat
Originally used with PLUMED version: 2.8
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

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1433,857 

opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d PACEthe frequency for kernel deposition=500000 BARRIERthe free energy barrier to be overcome=30 TEMP temperature=330
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=d PACEthe frequency for kernel deposition=500000 BARRIERthe free energy barrier to be overcome=30 TEMP temperature=330  SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS

uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=1.5 KAPPAthe force constant for the wall=1000.0

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1433 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=4,5,7,11,14,16,18,20,22,27,28,31,34,38,39,41,42,45,48,51,56,59,62,63,66,68,72,73,74,81,82,84,86,90,92,93,97,100,101,104,108,110,113,117,118,122,123,126,129,132,136,142,147,149,154,157,161,163,166,168,169,177,181,186,189,196,197,200,207,208,210,213,214,219,222,224,226,232,236,238,241,248,250,251,253,256,258,262,263,265,268,276,278,281,285,287,289,292,296,299,301,304,308,309,314,318,319,321,326,332,334,336,338,339,340,343,352,354,358,360,361,364,367,369,373,377,380,382,383,386,393,395,397,402,404,408,412,415,418,419,422,428,429,432,434,436,438,443,446,451,453,455,461,466,469,472,474,475,478,481,489,492,494,495,497,502,505,506,512,516,519,520,524,525,531,532,535,540,541,549,551,555,558,561,563,565,566,572,577,579,582,585,589,595,597,600,603,607,609,613,615,616,619,622,625,627,633,634,637,641,646,647,653,657,659,661,664,668,670,672,674,678,679,684,686,691,692,694,696,698,703,704,709,713,715,717,719,721,726,729,730,736,740,742,748,749,750,752,758,760,761,764,766,767,771,775,778,779,781,783,786,789,796,797,798,804,807,812,816,819,824,827,835,837,840,843,848,852,858,862,865,866,867,869,872,875,877,879,882,884,886,889,891,895,899,902,903,907,910,913,915,919,922,925,928,930,935,937,942,944,946,950,955,957,961,963,968,970,974,975,979,983,987,989,993,995,997,999,1002,1008,1009,1013,1016,1018,1021,1024,1027,1031,1033,1034,1036,1044,1048,1049,1050,1054,1055,1060,1064,1065,1068,1072,1075,1078,1082,1084,1086,1091,1093,1095,1098,1102,1106,1108,1112,1113,1117,1121,1123,1125,1128,1130,1133,1138,1141,1144,1147,1151,1153,1155,1157,1159,1162,1167,1169,1174,1176,1177,1181,1182,1187,1188,1192,1196,1198,1201,1207,1208,1209,1216,1219,1225,1226,1232,1237,1238,1240,1242,1245,1247,1253,1257,1261,1264,1266,1268,1271,1272,1277,1278,1280,1284,1285,1288,1289,1293,1294,1298,1299,1307,1309,1311,1317,1320,1322,1326,1327,1329,1333,1335,1337,1338,1344,1349,1352,1357,1360,1367,1369,1374,1377,1380,1383,1389,1393,1394,1396,1397,1401,1403,1406,1407,1408,1413,1414,1416,1417,1420,1421,1423,1430,1432,1435,1438,1441,1444,1448,1450,1451,1454,1456,1465,1467,1468,1471,1474,1477,1483,1485,1488,1491,1494,1497,1498,1501,1505,1507,1512,1513,1517,1518,1520,1523,1526,1530,1533,1535,1537,1539,1542,1546,1548,1554,1555,1559,1562,1565,1566,1570,1573,1576,1577,1580,1584,1586,1591,1592,1601,1605,1607,1609,1611,1615,1619,1621,1624,1629,1630,1634,1639,1640,1643,1645,1649,1651,1654,1658,1659,1667,1669,1673,1674,1679,1681,1682,1687,1691,1692,1693,1695,1698,1701,1703,1705,1707,1711,1713,1716,1719,1723,1724,1727,1728,1729,1731,1737,1740,1742,1746,1750,1753,1756,1758,1762,1764,1769,1772,1776,1778,1781,1783,1785,1789,1791,1794,1796,1802,1806,1808,1810,1813,1815,1819,1824,1825,1827,1828,1834,1835,1837,1839,1842,1850,1854,1855,1859,1860,1864,1867,1869,1871,1874,1875,1879,1883,1886,1888,1890,1893,1899,1900,1902,1907,1909,1914,1916,1919,1920,1924,1926,1929,1934,1937,1940,1943,1947,1948,1955,1956,1959,1964,1967,1968,1971,1974,1977,1982,1985,1987,1989,1991,1998,2002,2006,2008,2010,2017,2018,2021,2024,2026,2028,2035,2037,2040,2041,2046,2049,2052,2055,2057,2061,2065,2067,2071,2074,2080,2083,2086,2088,2091,2092,2094,2098,2101,2105,2110,2115,2119,2121,2124,2125,2129,2132,2135,2138,2141,2143,2147,2150,2154,2157,2159,2160,2164,2168,2170,2175,2177,2178,2180,2185,2188,2190,2191,2196,2200,2202,2207,2209,2213,2217,2220,2221,2225,2228,2230,2232,2234,2237,2241,2242,2245,2247,2250,2253,2258,2262,2263,2267,2270,2275,2278,2280,2282,2288,2290,2293,2296,2303,2306,2314,2315,2317,2322,2324,2327,2328,2336,2338,2340,2344,2348,2351,2353,2355,2357,2360,2366,2370,2371,2373,2377,2380,2382,2386,2389,2391,2393,2400,2402,2403,2406,2410,2414,2415,2420,2424,2425,2429,2430,2434,2439,2441,2448,2451,2454,2458,2460,2461,2464,2465,2469,2471,2475,2476,2481,2482,2487,2488,2494,2495,2499,2501,2503,2508,2511,2514,2518,2519,2521,2523,2527,2528,2531,2536,2543,2544,2547,2550,2555,2558,2559,2562,2564,2565,2570,2574,2575,2577,2579,2584,2586,2587,2588,2593,2596,2600,2601,2604,2606,2611,2613,2616,2618,2624,2626,2631,2633,2636,2639,2642,2644,2646,2653,2654,2659,2662,2664,2670,2671,2675,2678,2680,2682,2686,2688,2689,2692,2695,2698,2699,2700,2701,2704,2708,2711,2715,2719,2722,2726,2731,2732,2735,2744,2745,2746,2750,2753,2756,2761,2764,2765,2767,2769,2774,2781,2782,2783,2785,2788,2789,2791,2795,2798,2800,2802,2804,2809,2814,2815,2817,2818,2823,2825,2827,2833,2835,2837,2839,2841,2846,2847,2850,2851,2855,2857,2861,2863,2866,2869,2873,2876,2877,2880,2883,2887,2889,2892,2894,2900,2902,2906,2910,2913,2919,2921,2923,2925,2931,2933,2935,2940,2942,2945,2947,2949,2953,2956,2960,2961,2962,2964,2967,2970,2973,2977,2981,2984,2986,2988,2990,2993,2998,3001,3003,3007,3010,3012,3015,3020,3023,3026,3029,3031,3035,3037,3039,3040,3042,3045,3048,3051,3055,3056,3060,3064,3066,3071,3075,3077,3079,3083,3085,3087,3090,3097,3099,3100,3105,3108,3112,3115,3117,3119,3123,3126,3127,3132,3133,3135,3136,3137,3140,3144,3148,3150,3153,3156,3161,3162,3166,3169,3173,3175,3179,3187,3189,3190,3194,3196,3201,3204,3205,3209,3213,3215,3218,3220,3225,3228,3231,3233,3236,3237,3241,3246,3248,3250,3254,3257,3259,3260,3263,3268,3270,3274,3276,3279,3281,3285,3288,3290,3296,3300,3302,3311,3312,3315,3317,3319,3325,3326,3327,3331,3334,3337,3339,3343,3345,3347,3350,3353,3356,3359,3364,3367,3371,3372,3373,3374,3377,3380,3383,3386,3388,3395,3398,3401,3403,3404,3410,3413,3416,3418,3422,3427,3430,3431,3435,3436,3438,3444,3445,3449,3452,3454,3459,3461,3468,3472,3475,3478,3482,3486,3492,3493,3496,3499,3502,3504,3507,3508,3513,3516,3519,3523,3525,3527,3530,3533,3534,3539,3543,3545,3549,3551,3555,3560,3564,3565,3567,3569,3573,3574,3579,3581,3585,3588,3591,3598,3599,3600,3603,3607,3609,3611,3614,3616,3619,3620,3622,3623,3628,3631,3636,3639,3641,3647,3648,3650,3654,3658,3662,3664,3666,3667,3672,3674,3676,3678,3681,3685,3687,3693,3695,3698,3703,3706,3710,3712,3713,3717,3719,3721,3728,3730,3732,3734,3738,3740,3743,3747,3750,3753,3757,3759,3761,3762,3763,3767,3770,3772,3773,3777,3781,3783,3785,3786,3788,3792,3793,3795,3798,3801,3805,3806,3807,3811,3814,3816,3817,3821,3823,3828,3834,3835,3838,3845,3847,3849,3852,3856,3859,3863,3867,3874,3876,3879,3885,3889,3891,3893,3896,3900,3902,3908,3910,3914,3918,3921,3923,3924,3926,3930,3932,3935,3939,3941,3944,3947,3948,3951,3954,3956,3959,3963,3965,3966,3969,3972,3974,3976,3980,3984,3987,3990,3992,3997,3998,4000,4004,4007,4010,4016,4018,4021,4023,4027,4030,4033,4036,4037,4039,4043,4044,4049,4053,4055,4057,4059,4063,4067,4070,4072,4079,4080,4084,4086,4090,4095,4096,4098,4099,4100,4104,4107,4110,4112,4118,4122,4125,4129,4130,4133,4138,4141,4146,4147,4153,4154,4158,4159,4164,4166,4168,4172,4174,4181,4183,4186,4187,4190,4193,4196,4198,4201,4205,4207,4210,4212,4215,4217,4219,4222,4228,4231,4234,4236,4238,4239,4243,4247,4253,4255,4257,4261,4265,4266,4268,4273,4275,4279,4283,4288,4292,4293,4295,4297,4300,4304,4308,4312,4313,4316,4317,4319,4323,4326,4333,4334,4338,4340,4343,4345,4349,4351,4354,4356,4359,4362,4366,4369,4371,4377,4381,4384,4387,4391,4396,4401,4402,4405,4407,4411,4412,4419,4421,4424,4426,4429,4432,4435,4436,4440,4442,4445,4448,4452,4454,4458,4460,4461,4462,4468,4471,4472,4474,4476,4478,4481,4488,4491,4492,4496,4500,4502,4508,4509,4515,4516,4521,4522,4528,4530,4531,4535,4537,4541,4543,4547,4549,4551,4554,4557,4559,4563,4567,4571,4573,4574,4577,4582,4583,4587,4588,4592,4594,4598,4601,4602,4605,4607,4611,4613,4615,4623,4625,4628,4631,4635,4637,4640,4643,4647,4648,4650,4651,4655,4659,4663,4664,4666,4670,4675,4676,4677,4683,4688,4690,4692,4694,4697,4701,4703,4707,4709,4711,4714,4715,4717,4721,4723,4726,4730,4733 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.25 D_MAX=0.375}

The COORDINATION action with label  calculates the following quantities:
 Quantity   
 Description  
.value
the value of the coordinationPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR