Hi Amber users,
However, I am doing NVT simulationsI notice that my TIB3P box deforms
during MD simulations, any idea?? below is my input file
QM/MM equilibration NVT with some restraints on the solute for 100ps
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
taup = 2,
cut = 10,
tempi = 100.0, temp0 = 300.0,
ntc=2,
ntf=2,
ntt = 3,
tol = 0.0001,
iwrap = 1,
ntt = 3,
gamma_ln = 1.0,
scee= 1.2,
nstlim =50000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
ntr = 1, restraint_wt=2.0, restraintmask=':1-186',
ifqnt=1
/
&qmmm
iqmatoms=
1132,1133,1134,1135,1136,1137,2582,2583,2584,2585,2586,2587,2588,2772,2773,2774,2775,2776,2777,2778,2779,2780,2781,2782,2783,2784,2785,2786,2787,2788,2789,2790,2791,2792,2793,2794,2795,2796,2797,2798,2799,2800,2801,2802,2803,2804,2805,2806,2807,2808,2809,2810,2811,2812,2813,2814,2815,2816,2817,2818,2819,
qmcharge=-1,
qm_theory='AM1',
qmcut=8.0,
writepdb=1
qmshake=0,
/
Thanks
Mahmoud
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Received on Mon Mar 28 2011 - 07:00:03 PDT
