I don't understand the box twist- are you saying the box dimensions change
in PBC, or your molecule moves?
have you evaluated the energy?
could it be a periodic imaging problem? there is lots of info on this in the
archives. you should use the ptraj image command- but it isn't clear quite
what you want to see, and if you understand how the PBC imaging works.
On Tue, Aug 23, 2011 at 4:53 PM, Bin Wu <wubin2002.gmail.com> wrote:
> Dear Amber Users
>
> I have observed a very strange phenomenon from trajectory visualization
> using VMD. I have attached the GIF format of the trajectory animations
> with
> this email. Owing to the fact that this mailing list limits the size of the
> attachment less than 1024KB, the quality of the GIF is very poor. Movies of
> higher qualities are listed with the following links:
>
> http://dl.dropbox.com/u/5951953/1.mpg
>
> http://dl.dropbox.com/u/5951953/1.gif
>
> Please check them out.
>
>
> I am simulating a polymer solvated in the truncated octahedral box under
> NPT
> ensemble. The Langenvin dynamics is invoked to control the temperature. The
> input script is actually copied from one official tutorial listed in Amber
> Website and is presented below.
>
> polyA-polyT 10-mer: 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0, ig = -1,
> nstlim = 500000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
>
> The abnormal phenomenon is that the simulation box suddenly changes its
> shape like twisting within very short time step intervals. In the movie
> attached, just the solute part is included in order to enable the audience
> to have a better view. And this kind of twist keeps happening along the
> simulation.
>
> In my opinion, the dynamics of the polymer should not be that fast. That is
> why I think it is very strange. I wonder weather what I saw is artifact and
> if it is could anybody tell me how to get rid of them.
>
> Any comments or suggestions would be highly appreciated.
>
> Thank you very much for your time.
>
> Best Regards!
>
> Bin
>
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Received on Tue Aug 23 2011 - 14:00:06 PDT
