Hi,
are you sure this isn't just the usual neighbouring box diffusion problem?
Did you look at your raw trajectory or did you use ptraj to image it back
into the original box before visualisation?
Thomas
On Mon, March 28, 2011 10:02 am, Mahmoud Soliman 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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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Mar 28 2011 - 07:30:02 PDT
