# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001
The UNITS action with label calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=./group_indices.dat
# INCLUDE FILE=./group_indices.dat
The INCLUDE action with label ./group_indices.dat calculates somethingLi: 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=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,1059,1060,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,1082,1083,1084,1085,1086,1087,1088,1089,1090,1091,1092,1093,1094,1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1132,1133,1134,1135,1136,1137,1138,1139,1140,1141,1142,1143,1144,1145,1146,1147,1148,1149,1150,1151,1152,1153,1154,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,1216,1217,1218,1219,1220,1221,1222,1223,1224,1225,1226,1227,1228,1229,1230,1231,1232,1233,1234,1235,1236,1237,1238,1239,1240,1241,1242,1243,1244,1245,1246,1247,1248,1249,1250,1251,1252,1253,1254,1255,1256,1257,1258,1259,1260,1261,1262,1263,1264,1265,1266,1267,1268,1269,1270,1271,1272,1273,1274,1275,1276,1277,1278,1279,1280,1281,1282,1283,1284,1285,1286,1287,1288,1289,1290,1291,1292,1293,1294,1295,1296,1297,1298,1299,1300,1301,1302,1303,1304,1305,1306,1307,1308,1309,1310,1311,1312,1313,1314,1315,1316,1317,1318,1319,1320,1501,1502,1503,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1516,1517,1518,1519,1520,1521,1522,1523,1524,1525,1526,1527,1528,1529,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1569,1570,1571,1572,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1585,1586,1587,1588,1589,1590,1591,1592,1593,1594,1595,1596,1597,1598,1599,1600,1601,1602,1603,1604,1605,1606,1607,1608,1609,1610,1611,1612,1613,1614,1615,1616,1617,1618,1619,1620,1621,1622,1623,1624,1625,1626,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1650,1651,1652,1653,1654,1655,1656,1657,1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1683,1684,1685,1686,1687,1688,1689,1690,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702,1703,1704,1705,1706,1707,1708,1709,1710,1711,1712,1713,1714,1715,1716,1717,1718,1719,1720,1721,1722,1723,1724,1725,1726,1727,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748,1749,1750,1751,1752,1753,1754,1755,1756,1757,1758,1759,1760,1761,1762,1763,1764,1765,1766,1767,1768,1769,1770,1771,1772,1773,1774,1775,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,1786,1787,1788,1789,1790,1791,1792,1793,1794,1795,1796,1797,1798,1799,1800,1801,1802,1803,1804,1805,1806,1807,1808,1809,1810,1811,1812,1813,1814,1815,1816,1817,1818,1819,1820,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026,2027,2028,2029,2030,2031,2032,2033,2034,2035,2036,2037,2038,2039,2040,2041,2042,2043,2044,2045,2046,2047,2048,2049,2050,2051,2052,2053,2054,2055,2056,2057,2058,2059,2060,2061,2062,2063,2064,2065,2066,2067,2068,2069,2070,2071,2072,2073,2074,2075,2076,2077,2078,2079,2080,2081,2082,2083,2084,2085,2086,2087,2088,2089,2090,2091,2092,2093,2094,2095,2096,2097,2098,2099,2100,2101,2102,2103,2104,2105,2106,2107,2108,2109,2110,2111,2112,2113,2114,2115,2116,2117,2118,2119,2120,2121,2122,2123,2124,2125,2126,2127,2128,2129,2130,2131,2132,2133,2134,2135,2136,2137,2138,2139,2140,2141,2142,2143,2144,2145,2146,2147,2148,2149,2150,2151,2152,2153,2154,2155,2156,2157,2158,2159,2160,2161,2162,2163,2164,2165,2166,2167,2168,2169,2170,2171,2172,2173,2174,2175,2176,2177,2178,2179,2180,2181,2182,2183,2184,2185,2186,2187,2188,2189,2190,2191,2192,2193,2194,2195,2196,2197,2198,2199,2200,2201,2202,2203,2204,2205,2206,2207,2208,2209,2210,2211,2212,2213,2214,2215,2216,2217,2218,2219,2220,2221,2222,2223,2224,2225,2226,2227,2228,2229,2230,2231,2232,2233,2234,2235,2236,2237,2238,2239,2240,2241,2242,2243,2244,2245,2246,2247,2248,2249,2250,2251,2252,2253,2254,2255,2256,2257,2258,2259,2260,2261,2262,2263,2264,2265,2266,2267,2268,2269,2270,2271,2272,2273,2274,2275,2276,2277,2278,2279,2280,2281,2282,2283,2284,2285,2286,2287,2288,2289,2290,2291,2292,2293,2294,2295,2296,2297,2298,2299,2300,2301,2302,2303,2304,2305,2306,2307,2308,2309,2310,2311,2312,2313,2314,2315,2316,2317,2318,2319,2320,2501,2502,2503,2504,2505,2506,2507,2508,2509,2510,2511,2512,2513,2514,2515,2516,2517,2518,2519,2520,2521,2522,2523,2524,2525,2526,2527,2528,2529,2530,2531,2532,2533,2534,2535,2536,2537,2538,2539,2540,2541,2542,2543,2544,2545,2546,2547,2548,2549,2550,2551,2552,2553,2554,2555,2556,2557,2558,2559,2560,2561,2562,2563,2564,2565,2566,2567,2568,2569,2570,2571,2572,2573,2574,2575,2576,2577,2578,2579,2580,2581,2582,2583,2584,2585,2586,2587,2588,2589,2590,2591,2592,2593,2594,2595,2596,2597,2598,2599,2600,2601,2602,2603,2604,2605,2606,2607,2608,2609,2610,2611,2612,2613,2614,2615,2616,2617,2618,2619,2620,2621,2622,2623,2624,2625,2626,2627,2628,2629,2630,2631,2632,2633,2634,2635,2636,2637,2638,2639,2640,2641,2642,2643,2644,2645,2646,2647,2648,2649,2650,2651,2652,2653,2654,2655,2656,2657,2658,2659,2660,2661,2662,2663,2664,2665,2666,2667,2668,2669,2670,2671,2672,2673,2674,2675,2676,2677,2678,2679,2680,2681,2682,2683,2684,2685,2686,2687,2688,2689,2690,2691,2692,2693,2694,2695,2696,2697,2698,2699,2700,2701,2702,2703,2704,2705,2706,2707,2708,2709,2710,2711,2712,2713,2714,2715,2716,2717,2718,2719,2720,2721,2722,2723,2724,2725,2726,2727,2728,2729,2730,2731,2732,2733,2734,2735,2736,2737,2738,2739,2740,2741,2742,2743,2744,2745,2746,2747,2748,2749,2750,2751,2752,2753,2754,2755,2756,2757,2758,2759,2760,2761,2762,2763,2764,2765,2766,2767,2768,2769,2770,2771,2772,2773,2774,2775,2776,2777,2778,2779,2780,2781,2782,2783,2784,2785,2786,2787,2788,2789,2790,2791,2792,2793,2794,2795,2796,2797,2798,2799,2800,2801,2802,2803,2804,2805,2806,2807,2808,2809,2810,2811,2812,2813,2814,2815,2816,2817,2818,2819,2820,3001,3002,3003,3004,3005,3006,3007,3008,3009,3010,3011,3012,3013,3014,3015,3016,3017,3018,3019,3020,3021,3022,3023,3024,3025,3026,3027,3028,3029,3030,3031,3032,3033,3034,3035,3036,3037,3038,3039,3040,3041,3042,3043,3044,3045,3046,3047,3048,3049,3050,3051,3052,3053,3054,3055,3056,3057,3058,3059,3060,3061,3062,3063,3064,3065,3066,3067,3068,3069,3070,3071,3072,3073,3074,3075,3076,3077,3078,3079,3080,3081,3082,3083,3084,3085,3086,3087,3088,3089,3090,3091,3092,3093,3094,3095,3096,3097,3098,3099,3100,3101,3102,3103,3104,3105,3106,3107,3108,3109,3110,3111,3112,3113,3114,3115,3116,3117,3118,3119,3120,3121,3122,3123,3124,3125,3126,3127,3128,3129,3130,3131,3132,3133,3134,3135,3136,3137,3138,3139,3140,3141,3142,3143,3144,3145,3146,3147,3148,3149,3150,3151,3152,3153,3154,3155,3156,3157,3158,3159,3160,3161,3162,3163,3164,3165,3166,3167,3168,3169,3170,3171,3172,3173,3174,3175,3176,3177,3178,3179,3180,3181,3182,3183,3184,3185,3186,3187,3188,3189,3190,3191,3192,3193,3194,3195,3196,3197,3198,3199,3200,3201,3202,3203,3204,3205,3206,3207,3208,3209,3210,3211,3212,3213,3214,3215,3216,3217,3218,3219,3220,3221,3222,3223,3224,3225,3226,3227,3228,3229,3230,3231,3232,3233,3234,3235,3236,3237,3238,3239,3240,3241,3242,3243,3244,3245,3246,3247,3248,3249,3250,3251,3252,3253,3254,3255,3256,3257,3258,3259,3260,3261,3262,3263,3264,3265,3266,3267,3268,3269,3270,3271,3272,3273,3274,3275,3276,3277,3278,3279,3280,3281,3282,3283,3284,3285,3286,3287,3288,3289,3290,3291,3292,3293,3294,3295,3296,3297,3298,3299,3300,3301,3302,3303,3304,3305,3306,3307,3308,3309,3310,3311,3312,3313,3314,3315,3316,3317,3318,3319,3320,3501,3502,3503,3504,3505,3506,3507,3508,3509,3510,3511,3512,3513,3514,3515,3516,3517,3518,3519,3520,3521,3522,3523,3524,3525,3526,3527,3528,3529,3530,3531,3532,3533,3534,3535,3536,3537,3538,3539,3540,3541,3542,3543,3544,3545,3546,3547,3548,3549,3550,3551,3552,3553,3554,3555,3556,3557,3558,3559,3560,3561,3562,3563,3564,3565,3566,3567,3568,3569,3570,3571,3572,3573,3574,3575,3576,3577,3578,3579,3580,3581,3582,3583,3584,3585,3586,3587,3588,3589,3590,3591,3592,3593,3594,3595,3596,3597,3598,3599,3600,3601,3602,3603,3604,3605,3606,3607,3608,3609,3610,3611,3612,3613,3614,3615,3616,3617,3618,3619,3620,3621,3622,3623,3624,3625,3626,3627,3628,3629,3630,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,3645,3646,3647,3648,3649,3650,3651,3652,3653,3654,3655,3656,3657,3658,3659,3660,3661,3662,3663,3664,3665,3666,3667,3668,3669,3670,3671,3672,3673,3674,3675,3676,3677,3678,3679,3680,3681,3682,3683,3684,3685,3686,3687,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,3708,3709,3710,3711,3712,3713,3714,3715,3716,3717,3718,3719,3720,3721,3722,3723,3724,3725,3726,3727,3728,3729,3730,3731,3732,3733,3734,3735,3736,3737,3738,3739,3740,3741,3742,3743,3744,3745,3746,3747,3748,3749,3750,3751,3752,3753,3754,3755,3756,3757,3758,3759,3760,3761,3762,3763,3764,3765,3766,3767,3768,3769,3770,3771,3772,3773,3774,3775,3776,3777,3778,3779,3780,3781,3782,3783,3784,3785,3786,3787,3788,3789,3790,3791,3792,3793,3794,3795,3796,3797,3798,3799,3800,3801,3802,3803,3804,3805,3806,3807,3808,3809,3810,3811,3812,3813,3814,3815,3816,3817,3818,3819,3820
The GROUP action with label Li calculates somethingNa: 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=1-4000:1 REMOVEremove these atoms from the list=Li
The GROUP action with label Na calculates somethingN: 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=4001,4002
# --- End of included input ---
The GROUP action with label N calculates somethingdn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=N
The DISTANCE action with label dn calculates the following quantities:| Quantity | Description |
| dn.value | the DISTANCE between this pair of atoms |
c1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Li R_0The r_0 parameter of the switching function=4.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0} MEAN calculate the mean of all the quantities
The COORDINATIONNUMBER action with label c1 calculates the following quantities:| Quantity | Description |
| c1.min | the minimum colvar |
| c1.max | the maximum colvar |
| c1.mean | the mean of the colvars |
| c1.value | the coordination numbers of the specified atoms |
c2: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Na R_0The r_0 parameter of the switching function=4.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0} MEAN calculate the mean of all the quantities
The COORDINATIONNUMBER action with label c2 calculates the following quantities:| Quantity | Description |
| c2.min | the minimum colvar |
| c2.max | the maximum colvar |
| c2.mean | the mean of the colvars |
| c2.value | the coordination numbers of the specified atoms |
uwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dn ATthe positions of the wall=10.0 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2.0
The UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Description |
| uwall.bias | the instantaneous value of the bias potential |
| uwall.force2 | the instantaneous value of the squared force due to this bias potential |
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes1
ARGthe labels of the scalars on which the bias will act=dn
FILE a file in which the list of all deposited kernels is stored=Kernels1.data
TEMP temperature=600
PACEthe frequency for kernel deposition=200
BARRIERthe free energy barrier to be overcome=150
RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD_EXPLORE
The OPES_METAD_EXPLORE action with label opes1 calculates the following quantities:| Quantity | Description |
| opes1.bias | the instantaneous value of the bias potential |
| opes1.rct | estimate of c(t) |
| opes1.zed | estimate of Z_n |
| opes1.neff | effective sample size |
| opes1.nker | total number of compressed kernels used to represent the bias |
PRINTPrint 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=50 FILEthe name of the file on which to output these quantities=COLVAR
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1
