This is not a good input for a constant volume simulation. Many things need
changing. Have you looked at the tutorials?
On May 14, 2016 3:49 PM, "Iqbal, Muhammad Sajid" <iqbal.uleth.ca> wrote:
> Dear amber community,
>
> I performed MD simulations on a box of dimension 300 x 300 x 300. I defined
> the dimensions using the following command.
>
> setbox mybox vdw
>
> I noticed that, as MD simulations proceed, the box dimension are changing.
> My first frame has the following dimension, generated by vmd.
>
>
> min1 = (1.2740000486373901, 1.4450000524520874, 1.0440000295639038)
> max1 = (302.4549865722656, 302.99700927734375, 302.3590087890625)
> total = ( 301.181, 301.552, 301.315 )
>
>
> and the final frame has the following dimensions after completing 125000
> steps.
>
> min2 = Vector(1.371000051498413, -6.394000053405762, -1.9179999828338623)
> max2 = Vector(305.86700439453125, 305.4129943847656, 306.697998046875)
> total= ( 304.496, 311.807, 308.616 )
>
> If I perform additional 10times steps, the dimension keeping changing to a
> very large number. Could any one please guide me how I can keep the
> dimensions fix to 300x300x300 throughout the simulations.
>
> Here is my MD script.
>
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100, ntwr = 8000
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 125000, dt = 0.001,
> cut = 999
>
> Regard,
> Sajid
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Received on Sat May 14 2016 - 13:00:04 PDT
