Hi Jason!
It tried and it doesn't work.
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.
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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Received on Tue Nov 11 2014 - 08:00:02 PST
