Date: Tue, 11 Nov 2014 17:24:03 +0100
Hi Dan,
1) No prior RMS-fitting.
2) Yes, using autoimage, at some point, the DNA strands are still separated.
3) I'm attaching a couple of pictures.
But I found the problem. It was the version of cpptraj. I got the
problem using v12.1.
Using version 15.01 the problem is solved!!!
Thank you very much!
Best,
P.
On 11/11/2014 05:05 PM, Daniel Roe wrote:
> 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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>
>
-- 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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