See Per Jr. Greisen comments to your previous message.
On Mon, Mar 28, 2011 at 6:02 PM, Mahmoud Soliman <mahmoudelkot.gmail.com> wrote:
> 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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--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Mon Mar 28 2011 - 07:30:03 PDT
