# # QMMM calculation for a complex reaction coordinate. # In this step we will move two protons each with one linear combination of distances. # In order to avoid the loss of important hydrogen bonds due to de harmonic force aplied on a part of the system a DISTANCE restriction with a very small harmonic will be applied on the atoms involved in the hydrogen bond. # QMMM &cntrl ntx = 7, irest = 1, ntrx = 1, ntxo = 1, nmropt = 0, ntpr = 100, ntwx =100, ntf = 1, ntb = 2, dielc = 1.0, cut = 9., nsnb = 10, imin = 0, ibelly = 0, iwrap = 1, nstlim = 20000, dt = 0.0005, temp0 = 300.0, tempi = 300.0, ntt = 1, vlimit = 20.0, ntp = 1, ntc = 1, tol = 0.00001, pres0=1, comp=44.6, jfastw=0, nscm=1000, ifqnt=1, / &qmmm iqmatoms=157,158,159,160,161,162,163,164,271,272,273,274,275,276,277,278,279,280,281,282,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,1213,1214,1215,1216,1217,1218,1219,1220,1289,1290,1291,1292,1293,1294,1295,1296,1297,1298,1299,1585,1586,1587,1588,1589,1590,1591,1592,1593,1594,1595,1596,1622,1623,1624,1625,1626,1627,1628,1629,1702,1703,1704,1705,1706,1707,1708,1709,1710,1711,1712,1713,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,1786,1787,3706,3707,3708,3709,3710,3711,6952,6953,6954,6955,6956,6957,6958,6959,6960,6961,6962,6963,6964,6965,6966,6967,6968,6969,6970,6971,6972,6973,6990,6991,6992,49716,49717,49718, qmcharge=+2, qm_theory='DFTB', qmshake=0, diag_routine=0, dftb_telec=100, qmcut=8.0, qmshake=0, writepdb= 1, &end &wt type='DUMPFREQ', istep1=5, &end &wt type="END", &end DISANG=dist.dat DUMPAVE=dist.lis / ncsu_smd output_file = 'smd_1.txt' output_freq = 100 variable type = LCOD i = (49716,49717,49717,3710) r = (1.0,-1.0) path = (-0.78,0.78) harm = (1000.0) end variable output_file = 'smd_2.txt' output_freq = 100 variable type = LCOD i = (367,368,368,49716) r = (1.0,-1.0) path = (-0.83,0.83) harm = (750.0) end variable output_file = 'smd_3.txt' output_freq = 100 variable type = DISTANCE i = (277,6962) path = (2.80,2.80) harm = (5.0) end variable output_file = 'smd_4.txt' output_freq = 100 variable type = DISTANCE i = (6956,1590) path = (2.0,2.0) harm = (5.0) end variable end ncsu_smd