try center/image please
On 8/23/11 5:39 PM, Bin Wu wrote:
> 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
>>>>>
>>>>> _______________________________________________
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>>>>> 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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--
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 - 15:00:05 PDT
