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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 11 2014 - 07:30:03 PST
