It's a little weird what's happening here. Imaging issues (at least the
ones I've seen) manifest themselves, typically, as simple translations (all
the way to the other side of the periodic box). What I saw from your
video/animation are abrupt rotations, I think. This could still be an
imaging issue, especially if you're using a truncated octahedron (since
there are rotations used in the reimaging process, even though I *think*
they should be rotated back...).
You should check your energies, densities, and other thermodynamic
quantities of interest to make sure that you're getting values that make
sense. If your jumps in your movie are associated with jumps in your
thermodynamic quantities, then something is messed up. If not (and your
quantities are behaving nicely), then you likely have some form of
visualization artifact.
You can delete these by centering and reimaging your system, as well as
doing an RMS fit of your simulation (which will align all of your frames to
eliminate translational/rotational motions).
HTH,
Jason
On Tue, Aug 23, 2011 at 5:19 PM, Bin Wu <wubin2002.gmail.com> wrote:
> Hello Carlos
>
> Thank you very much for your reply.
>
> If you have not seen the animation with those links, please check them out.
> It is clear to see them better than I describe.
>
> I am using the NPT ensemble. The water molecules are very dispersed so I
> cann't really tell whether the dimension of the simulation box changed or
> not. But I am sure that the whole simulation system went through certain
> sudden deformation within a couple of time steps.
>
> As for whether it is the periodic imaging problem, to be honest, I do not
> know. That is why turn to this mailing list for help.
>
> And of course, I have went through the archive for answer. It is just that
> I
> have not found simliar cases.
>
> Thank you very much.
>
> Bin
>
>
>
> 2011/8/23 Carlos Simmerling <carlos.simmerling.gmail.com>
>
> > 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 23 2011 - 15:00:07 PDT
