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
>>>
>>>
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--
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 - 14:30:04 PDT
