Dear Prof. Adrian
Thank you very much for the suggestion.
I will try to use "image" for the trajectory analysis right now.
Thank you very much.
Bin
2011/8/23 Adrian Roitberg <roitberg.qtp.ufl.edu>
> Dear Bin
>
> I am pretty sure (specially after your comment on the waters being
> dispersed) that you have an imaging issue. See the list on how to
> image/center the polymer and the waters. What you are seeing is not a
> deformation (seems to me) but a rigid body rotation.
>
> Adrian
>
>
> On 8/23/11 5:19 PM, Bin Wu 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
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> >>
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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Received on Tue Aug 23 2011 - 15:00:04 PDT
