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qm_mm_setup_for_reaction_coordinate_calling_gaussian_as_extern_program [2016/03/07 14:24] (current)
root created
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 +**Here you can find an example of an input for running QM/MM using sander but treating the QM part with Gaussian. This procedure will allow you to increase the level of theory for the treatment of the QM part (and thereby, the computational cost :))**.\\
  
 +''​QM/​MM input calling Gaussian as external program''​\\
 +''​ &​cntrl''​\\
 +''​ ntx = 5, irest = 1, ntrx = 1,''​\\
 +''​ ntxo = 1, nmropt = 1,''​\\
 +''​ ntpr = 100, ntwx =100,''​\\
 +''​ ntf = 1, ntb = 2, dielc = 1.0,''​\\
 +''​ cut = 12., nsnb = 10,''​\\
 +''​ imin = 0, ibelly = 0, iwrap = 1,''​\\
 +''​ nstlim = 200, 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=178,​179,​180,​181,​182,​183,​184,​185,​186,​187,​188,​189,''​\\
 +''​196,​197,​198,​199,​200,​201,''​\\
 +''​1876,​1877,​1878,​1879,​1880,​1881,​1882,​1883,''​\\
 +''​1939,​1940,​1941,​1942,​1943,​1944,​1945,​1946,''​\\
 +''​1979,​1980,​1981,​1982,​1983,​1984,​1985,​1986,​1987,​1988,​1989,​1990,''​\\
 +''​2774,​2775,​2776,​2777,​2778,​2779,​2780,​2781,''​\\
 +''​3377,​3378,​3379,​3380,​3381,​3382,​3383,​3384,​3385,​3386,​3387,​3388,​3389,​3390,​3391,​3392,''​\\
 +''​3420,''​\\
 +''​6787,​6788,​6789,''​\\
 +''​6790,​6791,​6792,''​\\
 +''​qm_theory='​EXTERN',''​\\
 +''​qm_ewald=0,''​\\
 +''​qmcharge=-1,''​\\
 +''​spin=1,''​\\
 +''​writepdb= 1,''​\\
 +''/''​\\
 +''&​gau''​\\
 +''​ method='​B3LYP',''​\\
 +''​ basis='​6-311+G(2d,​2p)',''​\\
 +''​ num_threads=8,''​\\
 +NOTE: in case you need to specify special parameters (e.g. Zn2+ for DFT methods), activates the flag as ''​use_template=1''​ and incorporate those parameters in a file called //​gau_job.tpl//​ placed in the same folder were you are going to run your calculations.\\
 +''&​end''​\\
 +''/''​\\
 +''&​wt''​\\
 +''​type='​DUMPFREQ',​ istep1=5,''​\\
 +''&​end''​\\
 +''&​wt''​\\
 +''​type="​END",''​\\
 +''&​end''​\\
 +''/''​\\
 +''​ncsu_smd''​\\
 +\\
 +'' ​ output_file = '​extern.dat''​\\
 +'' ​ output_freq = 10''​\\
 +\\
 +''​ variable''​\\
 +''​ type = DISTANCE''​\\
 +''​ i = (187,​3377)''​\\
 +''​ path = (x,​1.00)''​\\
 +''​ harm = (1000.0)''​\\
 +''​ end variable''​\\
 +\\
 +''​variable''​\\
 +''​ type = LCOD''​\\
 +''​ i = (3381,​3378,​3378,​186)''​\\
 +''​ r = (1.0,​-1.0)''​\\
 +''​ path = (-1.9,​1.9)''​\\
 +''​ harm = (1000.0)''​\\
 +''​ end variable''​\\
 +~                             
qm_mm_setup_for_reaction_coordinate_calling_gaussian_as_extern_program.txt ยท Last modified: 2016/03/07 14:24 by root