Hi,
On Tue, Nov 11, 2014 at 8:59 AM, "Pablo D. Dans Puiggròs"
<pdans.mmb.pcb.ub.es> wrote:
> Actually, i visualized the full trajectory and i realized that the
> reimaging is doing something wrong also with the ions: they are taken
> from different boxes and are clearly not connected to the DNA. It looks
> like that without WAT the reimaging is not able to recognize the right
> box and it keeps going changing the reference box, even if the netcdf
> files contain all the information.
This is not correct. Imaging depends *only* on the box information
(i.e. the unit cell vectors). So a few questions:
1) Have you performed any RMS-fitting on this traectory at any point prior?
2) With 'autoimage' are the DNA strands still separated?
3) Can you clarify what you mean by the ions "are taken from different
boxes"? There is only one unit cell; if an ion is not in the main unit
cell then it is still interacting with the main unit cell. A picture
may help in this case.
-Dan
>
> Another suggestion? :-)
>
> Thanks,
> P
>
> On 11/11/2014 04:28 PM, Jason Swails wrote:
>> On Tue, Nov 11, 2014 at 10:24 AM, "Pablo D. Dans Puiggròs" <
>> pdans.mmb.pcb.ub.es> wrote:
>>
>>> Hi,
>>>
>>> I have a reimage problem with a double helix DNA trajectory (netCDF
>>> format).
>>>
>>> I ran a long simulation with several restart files. Since the simulation
>>> was very long, after each restart I removed the water molecules and
>>> stored each DNA+ions trajectory with this command (using cpptraj):
>>>
>>> trajin md12.nc 1 -1 1
>>> strip :WAT
>>> trajout md12_nowat.nc netcdf
>>>
>>> Now I want to join together all the pieces doing the usual reimaging.
>>> I've tried several commands in cpptraj like "autoimage familiar" or
>>> things like this:
>>>
>>> center :1-18 mass origin
>>> image origin center familiar
>>> center :1-36 mass origin
>>> image origin center familiar
>>>
>>> but unsuccessfully! At several frames during the full trajectory the two
>>> strands are separated. Any suggestion?
>>>
>> Try replacing the above set of commands with just "autoimage".
>>
>> HTH,
>> Jason
>>
>
>
> --
> Pablo D. Dans Puiggròs, PhD
> Joint BSC-CRG-IRB Research Program in Computational Biology
> Molecular Modeling and Bioinformatics Group - http://mmb.pcb.ub.es
> Institute for Research in Biomedicine (IRB Barcelona) - http://www.irbbarcelona.org
> Baldiri Reixac 10, 08028 Barcelona, Spain
> pablo.dans.irbbbarcelona.org
> pdans.mmb.pcb.ub.es
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Nov 11 2014 - 08:30:02 PST
