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From: Chunli Yan <utchunliyan.gmail.com>

Date: Wed, 4 Oct 2017 23:51:16 -0400

Thanks, Pan.

I will test the force constant.

Best,

*Chunli*

On Wed, Oct 4, 2017 at 11:33 PM, Feng Pan <fpan3.ncsu.edu> wrote:

*> Hi, Chunli
*

*>
*

*> The Muti_RMSD can be used for one group of atoms and your format should be
*

*> correct.
*

*>
*

*> For the anchor_strength, I think for COM_TORSION your 200 is large enough
*

*> but for the MULTI_RMSD 10 may be is a little bit small. You could do some
*

*> trial
*

*> runs to see if you need a larger strength.
*

*>
*

*> Best
*

*> Feng
*

*>
*

*> On Thu, Oct 5, 2017 at 10:57 AM, Chunli Yan <utchunliyan.gmail.com> wrote:
*

*>
*

*> > Hello,
*

*> >
*

*> > I define two collective variables in string methods below:
*

*> >
*

*> > file
*

*> >
*

*> > &colvar ! Pseudo-dihedral
*

*> >
*

*> > cv_type = 'COM_TORSION'
*

*> >
*

*> > cv_ni = 58, cv_i =
*

*> > 3335,3336,3338,3339,3340,3341,3344,3345,3347,3348,3399,3400,
*

*> > 3402,3403,3404,3405,3406,3408,3409,3412,3413,4066,4067,4069,
*

*> > 4071,4072,4075,4076,4077,4129,4130,4132,4133,4137,4138,4139,
*

*> > 4141,4142,0,3354,3355,3356,3357,3358,0,3386,3387,3388,
*

*> > 3389,3390,0,3367,3368,3370,3374,3378,3379,0
*

*> >
*

*> > anchor_position = 0.164365
*

*> >
*

*> > anchor_strength = 200.0
*

*> >
*

*> > /
*

*> >
*

*> > &colvar ! Glycosidic torsion
*

*> >
*

*> > cv_type = 'MULTI_RMSD'
*

*> >
*

*> > cv_ni = 196, cv_nr = 588, cv_i =
*

*> > 420,422,424,426,430,433,437,438,439,441,443,445,449,452,
*

*> > 456,457,458,460,463,464,465,467,469,471,475,478,482,483,
*

*> > 484,486,488,491,492,493,496,497,498,499,502,505,508,510,
*

*> > 511,512,514,517,518,519,521,523,526,528,532,536,537,538,
*

*> > 540,542,545,548,549,553,554,555,557,559,563,564,565,567,
*

*> > 569,573,574,575,577,579,582,583,585,587,588,590,592,594,
*

*> > 595,596,598,600,603,606,609,612,616,617,618,620,623,624,
*

*> > 625,627,629,632,633,634,636,638,640,641,642,644,646,649,
*

*> > 650,651,653,655,657,658,659,661,663,666,667,669,671,672,
*

*> > 674,676,678,679,680,681,684,687,690,692,693,694,696,699,
*

*> > 700,701,702,705,708,711,713,714,715,717,720,721,722,724,
*

*> > 726,729,730,731,734,735,1240,1242,1244,1246,1250,1252,1253,
*

*> > 1254,1256,1258,1261,1262,1263,1266,1267,1268,1270,1272,1275,
*

*> > 1278,1279,1283,1284,1285,1287,1289,1291,1295,1299,1300,1301,
*

*> > 1303,1305,1308,1311,1312,1313,1314,1315,1316,1318,1320,1323,
*

*> > 1326,1329,1331,1332,1335,1338,1339,1340,1342,1344,1346,1350,
*

*> > 1352,1353,1354,1356,1358,1360,1364,1366,1367,1368,1369,1372,
*

*> > 1375,1378,1380,1381,1382,1384,1387,1388,1389,1391,1393,1396,
*

*> > 1398,1399,1400,1402,1404,1407,1410,1413,1416,1420,1421,1422,
*

*> > 1424,1426,1429,1430,1431,1432,1433,1434,1436,1438,1441,1443,
*

*> > 1447,1451,1452,1453,1455,1457,1460,1462,1463,1464,1466,1468,
*

*> > 1471,1473,1474,1865,1867,1869,1871,1875,1879,1880,1881,1883,
*

*> > 1885,1888,1889,1891,1893,1895,1897,1899,1900,1901,1903,1905,
*

*> > 1908,1909,1910,1913,1914,1915,1917,1920,1921,1922,1924,1926,
*

*> > 1929,1932,1935,1938,1942,1943,1944,1946,1948,1951,1953,1954,
*

*> > 1955,1957,1959,1961,1965,1968,1972,1973,2535,2537,2539,2542,
*

*> > 2545,2546,2550,2551,2552,2553,2556,2559,2562,2564,2565,2566,
*

*> > 2568,2570,2573,2575,2576,2577,2579,2581,2584,2586,2587,2588,
*

*> > 2590,2592,2595,2597,2598,2599,2601,2603,2607,2608,2609,2611,
*

*> > 2613,2616,2619,2622,2624,2625,2628,2631,2632,2633,2635,2637,
*

*> > 2640,2642,2643,2644,2646,2648,2652,2653,2654,2656,2658,2661,
*

*> > 2664,2665,2666,2669,2670,2671,2673,2675,2678,2679,2681,2683,
*

*> > 2685,2687,2689,2690,2691,2692,2695,2698,2701,2703,2704,2705,
*

*> > 2707,2709,2712,2715,2718,2720,2721,2724,2727,2728,2729,2731,
*

*> > 2733,2737,2738,2739,2741,2743,2746,2749,2750,2751,2754,2755,
*

*> > 3323,3324,3325,3326,3327,3330,3332,3333,3335,3336,3338,3339,
*

*> > 3340,3341,3344,3345,3347,3348,3349,3351,3354,3355,3356,3357,
*

*> > 3358,3359,3362,3364,3365,3367,3368,3370,3371,3372,3373,3374,
*

*> > 3375,3378,3379,3380,3381,3383,3386,3387,3388,3389,3390,3391,
*

*> > 3394,3396,3397,3399,3400,3402,3403,3404,3405,3406,3408,3409,
*

*> > 3412,3413,3414,3416,3419,4054,4055,4056,4057,4058,4061,4063,
*

*> > 4064,4066,4067,4069,4071,4072,4075,4076,4077,4078,4080,4083,
*

*> > 4084,4085,4086,4087,4088,4091,4093,4094,4096,4097,4099,4100,
*

*> > 4101,4102,4103,4105,4106,4109,4110,4111,4113,4116,4117,4118,
*

*> > 4119,4120,4121,4124,4126,4127,4129,4130,4132,4133,4137,4138,
*

*> > 4139,4141,4142,4143,4145,4148
*

*> >
*

*> > cv_r =
*

*> > 34.27399826049805,60.42100143432617,38.21500015258789,35.
*

*> > 612998962402344,59.85200119018555,34.64500045776367,36.3120002746582,56.
*

*> > 362998962402344,33.18899917602539,38.138999938964844,55.
*

*> 50199890136719,29.
*

*> > 913999557495117,34.9119987487793,53.867000579833984,28.
*

*> 628999710083008,32.
*

*> > 2859992980957,51.393001556396484,30.055999755859375,34.0099983215332,47.
*

*> > 96500015258789,30.24799919128418,31.84000015258789,44.85100173950195,29.
*

*> > 577999114990234,30.697999954223633,44.16600036621094,33.
*

*> > 207000732421875,29.40399932861328,47.792999267578125,33.
*

*> 57400131225586,27.
*

*> > 777999877929688,47.547000885009766,30.100000381469727,26.
*

*> > 16200065612793,44.231998443603516,31.238000869750977,24.
*

*> > 788000106811523,45.42900085449219,34.64400100708008,23.
*

*> 73699951171875,48.
*

*> > 95500183105469,33.50600051879883,25.715999603271484,50.
*

*> 569000244140625,36.
*

*> > 417999267578125,29.128000259399414,52.191001892089844,37.
*

*> 1609992980957,32.
*

*> > 0359992980957,50.141998291015625,38.652000427246094,30.
*

*> 492000579833984,46.
*

*> > 678001403808594,39.33599853515625,32.85599899291992,43.
*

*> 87900161743164,40.
*

*> > 44200134277344,33.029998779296875,43.055999755859375,43.
*

*> 31999969482422,36.
*

*> > 86600112915039,43.21699905395508,42.95399856567383,36.85900115966797,46.
*

*> > 83599853515625,41.56800079345703,30.868000030517578,59.
*

*> 72999954223633,32.
*

*> > 85599899291992,33.505001068115234,58.435001373291016,30.
*

*> 3439998626709,35.
*

*> > 87699890136719,59.79800033569336,27.660999298095703,34.
*

*> 56399917602539,57.
*

*> > 21200180053711,25.104000091552734,31.024999618530273,55.
*

*> > 683998107910156,24.98200035095215,31.709999084472656,52.
*

*> 57699966430664,22.
*

*> > 893999099731445,31.83300018310547,49.60499954223633,25.
*

*> 31599998474121,34.
*

*> > 79800033569336,47.16600036621094,24.929000854492188,36.
*

*> 81100082397461,44.
*

*> > 582000732421875,26.996999740600586,39.23099899291992,47.
*

*> 40999984741211,27.
*

*> > 96299934387207,41.37799835205078,50.36800003051758,26.
*

*> 801000595092773,43.
*

*> > 28099822998047,48.426998138427734,24.02400016784668,40.
*

*> 49300003051758,48.
*

*> > 715999603271484,21.333999633789063,40.034000396728516,52.
*

*> > 44300079345703,21.554000854492188,41.49599838256836,53.
*

*> 99100112915039,18.
*

*> > 445999145507813,43.71900177001953,57.150001525878906,18.
*

*> > 288999557495117,38.277000427246094,62.9739990234375,38.
*

*> 763999938964844,40.
*

*> > 308998107910156,61.012001037597656,36.18899917602539,40.
*

*> 17399978637695,57.
*

*> > 24100112915039,37.03300094604492,43.882999420166016,56.
*

*> 60599899291992,36.
*

*> > 15399932861328,47.310001373291016,58.047000885009766,35.
*

*> 16699981689453,46.
*

*> > 50699996948242,56.73500061035156,31.64900016784668,43.
*

*> 242000579833984,58.
*

*> > 67399978637695,31.025999069213867,43.04199981689453,59.
*

*> 12300109863281,40.
*

*> > 840999603271484,44.94900131225586,55.805999755859375,41.
*

*> > 069000244140625,42.665000915527344,53.637001037597656,38.
*

*> > 88600158691406,39.71200180053711,51.957000732421875,40.6609992980957,40.
*

*> > 87699890136719,48.819000244140625,38.76900100708008,42.
*

*> 53799819946289,45.
*

*> > 902000427246094,40.56700134277344,43.28099822998047,44.9630012512207,38.
*

*> > 41899871826172,44.400001525878906,44.97600173950195,37.
*

*> 457000732421875,43.
*

*> > 856998443603516,44.86000061035156,36.02199935913086,43.
*

*> 11899948120117,43.
*

*> > 56700134277344,35.64799880981445,41.84000015258789,43.79499816894531,34.
*

*> > 82899856567383,41.95199966430664,44.91299819946289,33.86000061035156,40.
*

*> > 941001892089844,45.606998443603516,33.3650016784668,39.
*

*> 71799850463867,45.
*

*> > 178001403808594,33.50600051879883,41.06999969482422,46.
*

*> 75400161743164,32.
*

*> > 763999938964844,45.14799880981445,46.3129997253418,37.5629997253418,44.
*

*> > 52000045776367,47.33100128173828,37.23500061035156,47.
*

*> 183998107910156,47.
*

*> > 44200134277344,38.56999969482422,50.35599899291992,47.11899948120117,40.
*

*> > 82699966430664,50.733001708984375,49.05099868774414,43.
*

*> 97700119018555,47.
*

*> > 832000732421875,50.03499984741211,45.46500015258789,45.5099983215332,47.
*

*> > 8129997253418,44.270999908447266,43.86800003051758,46.31999969482422,47.
*

*> > 27799987792969,40.805999755859375,48.1150016784668,48.
*

*> 638999938964844,42.
*

*> > 02199935913086,50.189998626708984,51.63999938964844,44.
*

*> 516998291015625,38.
*

*> > 483001708984375,26.447999954223633,43.24300003051758,38.
*

*> 55099868774414,25.
*

*> > 68899917602539,45.79199981689453,38.40299987792969,25.
*

*> 708999633789063,44.
*

*> > 54800033569336,39.73899841308594,27.44700050354004,43.36199951171875,40.
*

*> > 10499954223633,28.1299991607666,43.54499816894531,41.117000579833984,29.
*

*> > 263999938964844,44.250999450683594,40.560001373291016,30.
*

*> > 364999771118164,45.06100082397461,41.571998596191406,30.
*

*> 93600082397461,46.
*

*> > 17300033569336,40.9379997253418,31.700000762939453,47.23699951171875,40.
*

*> > 19499969482422,31.23699951171875,47.88999938964844,39.
*

*> 558998107910156,32.
*

*> > 17399978637695,47.37099838256836,40.10300064086914,33.35100173950195,47.
*

*> > 689998626708984,39.99300003051758,34.729000091552734,48.
*

*> > 691001892089844,39.292999267578125,35.2239990234375,46.
*

*> 99100112915039,40.
*

*> > 6619987487793,35.654998779296875,46.00199890136719,41.41999816894531,35.
*

*> > 231998443603516,45.55400085449219,41.60599899291992,33.
*

*> 99399948120117,46.
*

*> > 32500076293945,40.94599914550781,33.07500076293945,44.
*

*> 202999114990234,42.
*

*> > 439998626708984,28.849000930786133,45.45800018310547,42.
*

*> 44900131225586,29.
*

*> > 742000579833984,43.23899841308594,43.4739990234375,29.11400032043457,43.
*

*> > 35100173950195,44.94599914550781,28.481000900268555,42.
*

*> 03499984741211,45.
*

*> > 619998931884766,28.392000198364258,44.01499938964844,45.
*

*> 03200149536133,27.
*

*> > 163000106811523,44.20199966430664,45.59400177001953,29.
*

*> 660999298095703,43.
*

*> > 645999908447266,45.520999908447266,30.98900032043457,44.
*

*> 37699890136719,46.
*

*> > 448001861572266,31.982999801635742,45.21699905395508,45.
*

*> 64799880981445,32.
*

*> > 84299850463867,46.57699966430664,46.13199996948242,32.
*

*> > 79899978637695,47.5,45.01499938964844,33.099998474121094,48.
*

*> > 04800033569336,44.23899841308594,32.0890007019043,48.92900085449219,43.
*

*> > 209999084472656,32.292999267578125,49.41999816894531,42.
*

*> 50699996948242,31.
*

*> > 143999099731445,48.887001037597656,42.742000579833984,30.
*

*> > 076000213623047,50.33100128173828,41.70899963378906,31.
*

*> 27899932861328,49.
*

*> > 236000061035156,42.9630012512207,33.59299850463867,50.0880012512207,41.
*

*> > 97800064086914,33.972999572753906,48.696998596191406,43.
*

*> 6349983215332,34.
*

*> > 59700012207031,47.792999267578125,44.691001892089844,34.
*

*> 38800048828125,47.
*

*> > 30099868774414,45.26900100708008,35.334999084472656,45.
*

*> 27899932861328,47.
*

*> > 50600051879883,31.30900001525879,46.65700149536133,46.
*

*> 858001708984375,31.
*

*> > 433000564575195,45.22999954223633,48.763999938964844,32.
*

*> 03300094604492,43.
*

*> > 87799835205078,49.683998107910156,31.94499969482422,42.
*

*> 63100051879883,48.
*

*> > 9739990234375,32.33000183105469,43.79899978637695,50.57600021362305,30.
*

*> > 76300048828125,44.231998443603516,50.612998962402344,33.
*

*> 21500015258789,44.
*

*> > 20000076293945,50.095001220703125,34.54499816894531,45.
*

*> 48699951171875,50.
*

*> > 3120002746582,35.35599899291992,46.41299819946289,49.2599983215332,35.
*

*> > 150001525878906,47.72700119018555,49.742000579833984,35.
*

*> 36899948120117,48.
*

*> > 68299865722656,48.88800048828125,34.6150016784668,48.83700180053711,48.
*

*> > 834999084472656,33.255001068115234,49.60200119018555,47.875,32.
*

*> > 8380012512207,50.05099868774414,47.255001068115234,34.
*

*> 012001037597656,50.
*

*> > 89799880981445,46.11000061035156,34.233001708984375,51.3849983215332,45.
*

*> > 31800079345703,33.4370002746582,51.1150016784668,45.8390007019043,35.
*

*> > 56399917602539,50.577999114990234,46.54399871826172,36.
*

*> 57400131225586,50.
*

*> > 56100082397461,45.89699935913086,37.70500183105469,49.
*

*> 742000579833984,47.
*

*> > 58300018310547,36.42900085449219,49.529998779296875,47.
*

*> 90800094604492,35.
*

*> > 11399841308594,46.20399856567383,51.650001525878906,35.1349983215332,47.
*

*> > 64699935913086,51.196998596191406,34.874000549316406,46.
*

*> > 018001556396484,52.45899963378906,36.29800033569336,59.
*

*> 125999450683594,40.
*

*> > 47200012207031,40.66299819946289,59.959999084472656,40.
*

*> 61600112915039,41.
*

*> > 87900161743164,58.84299850463867,39.12099838256836,40.
*

*> 138999938964844,57.
*

*> > 71500015258789,41.215999603271484,40.935001373291016,57.
*

*> 67900085449219,42.
*

*> > 446998596191406,41.64699935913086,56.26900100708008,42.9900016784668,41.
*

*> > 948001861572266,55.652000427246094,43.459999084472656,40.75,54.
*

*> > 32699966430664,42.96200180053711,40.678001403808594,53.
*

*> 92499923706055,42.
*

*> > 82699966430664,39.237998962402344,54.60499954223633,41.
*

*> 97800064086914,38.
*

*> > 4010009765625,54.290000915527344,41.92399978637695,37.
*

*> 082000732421875,53.
*

*> > 23899841308594,42.757999420166016,36.612998962402344,53.
*

*> 00600051879883,42.
*

*> > 81700134277344,35.32899856567383,52.59000015258789,43.61899948120117,37.
*

*> > 37900161743164,52.91899871826172,43.64799880981445,38.
*

*> 702999114990234,52.
*

*> > 26100158691406,44.41400146484375,39.40999984741211,55.32400131225586,41.
*

*> > 9900016784668,42.6349983215332,54.37799835205078,41.65999984741211,41.
*

*> > 48500061035156,54.66400146484375,42.617000579833984,43.
*

*> 74700164794922,53.
*

*> > 79600143432617,41.814998626708984,44.86000061035156,54.
*

*> 09400177001953,42.
*

*> > 39899826049805,46.18899917602539,53.95800018310547,40.35900115966797,44.
*

*> > 67300033569336,52.25299835205078,42.16299819946289,44.50299835205078,51.
*

*> > 63399887084961,43.36800003051758,44.94900131225586,50.0890007019043,43.
*

*> > 3390007019043,44.970001220703125,49.58100128173828,43.
*

*> 624000549316406,43.
*

*> > 67599868774414,49.058998107910156,42.46699905395508,43.
*

*> 05099868774414,49.
*

*> > 89799880981445,42.007999420166016,41.90599822998047,50.
*

*> 88199996948242,41.
*

*> > 04899978637695,41.89699935913086,51.207000732421875,40.
*

*> 611000061035156,40.
*

*> > 71200180053711,50.42599868774414,41.375999450683594,39.
*

*> 84400177001953,50.
*

*> > 30699920654297,41.38800048828125,38.40800094604492,50.85300064086914,40.
*

*> > 694000244140625,37.55500030517578,49.402000427246094,42.
*

*> 30500030517578,37.
*

*> > 93199920654297,48.66999816894531,43.125999450683594,38.
*

*> 72200012207031,47.
*

*> > 547000885009766,43.50199890136719,38.172000885009766,48.
*

*> 61600112915039,43.
*

*> > 01100158691406,40.04600143432617,49.59299850463867,42.20399856567383,40.
*

*> > 56700134277344,49.46699905395508,42.012001037597656,45.
*

*> 44499969482422,48.
*

*> > 8380012512207,41.43199920654297,44.16999816894531,48.599998474121094,42.
*

*> > 018001556396484,46.608001708984375,47.27899932861328,42.
*

*> > 930999755859375,46.86899948120117,47.590999603271484,44.
*

*> > 362998962402344,46.66899871826172,46.70000076293945,42.
*

*> 54600143432617,48.
*

*> > 18299865722656,46.20100021362305,42.48500061035156,45.75299835205078,45.
*

*> > 83599853515625,43.356998443603516,44.69300079345703,45.
*

*> 03900146484375,42.
*

*> > 7130012512207,43.54399871826172,45.904998779296875,42.
*

*> 347999572753906,42.
*

*> > 48099899291992,45.32600021362305,41.255001068115234,41.
*

*> 81700134277344,46.
*

*> > 27000045776367,40.608001708984375,40.8489990234375,47.23099899291992,39.
*

*> > 70100021362305,41.26100158691406,47.94300079345703,38.96900177001953,40.
*

*> > 361000061035156,49.00199890136719,38.0,40.861000061035156,47.
*

*> > 729000091552734,39.138999938964844,38.92599868774414,48.
*

*> 2859992980957,38.
*

*> > 5369987487793,38.01499938964844,46.8390007019043,40.130001068115234,38.
*

*> > 595001220703125,46.0989990234375,40.882999420166016,39.
*

*> 47800064086914,45.
*

*> > 32899856567383,41.736000061035156,39.029998779296875,44.
*

*> > 209999084472656,41.46500015258789,43.92499923706055,44.
*

*> 847999572753906,40.
*

*> > 41299819946289,43.01100158691406,42.82099914550781,41.56399917602539,43.
*

*> > 619998931884766
*

*> >
*

*> > anchor_position = 0.4964
*

*> >
*

*> > anchor_strength = 10.0
*

*> >
*

*> > /
*

*> >
*

*> > I want to know whether I use the right format and whether the
*

*> > anchor_strength is sufficient enough. And in "MULTI_RMSD", I only have
*

*> one
*

*> > group of atoms not multi groups of atoms. Can I still use "MULTI_RMSD" in
*

*> > the string part, is it the right format? cv_i are list of serial number
*

*> of
*

*> > atoms, cv_r are all coordinates of all corresponding atoms in the
*

*> reference
*

*> > structure.
*

*> >
*

*> > Thanks,
*

*> >
*

*> > Best,
*

*> >
*

*> >
*

*> > *Chunli*
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*> >
*

*>
*

*>
*

*>
*

*> --
*

*> Feng Pan
*

*> Ph.D. Candidate
*

*> North Carolina State University
*

*> Department of Physics
*

*> Email: fpan3.ncsu.edu
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Wed Oct 04 2017 - 21:00:04 PDT

Date: Wed, 4 Oct 2017 23:51:16 -0400

Thanks, Pan.

I will test the force constant.

Best,

*Chunli*

On Wed, Oct 4, 2017 at 11:33 PM, Feng Pan <fpan3.ncsu.edu> wrote:

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Received on Wed Oct 04 2017 - 21:00:04 PDT

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