Unless your trajectories are named with incrementing numbers coming at the
end of the trajectories, you need to use "trajnames" in the trajin command
to do this.
Note that (since I was lazy and wanted to get pH-REMD working quickly
several years ago) the pH is stored in trajectories as the "temperature",
specifically so that pH-REMD files could take advantage of existing tools
for processing T-REMD files. But your trajin line should look something
like this:
trajin name.ph01.nc trajnames name.ph02.nc,name.ph03.nc,...
Also, I suggest consulting some of the REMD tutorials to try and understand
how to analyze REMD trajectories (which is a little different than
analyzing "normal" trajectories).
HTH,
Jason
On Wed, Aug 24, 2016 at 7:19 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Hi,
>
>
> I want to rebuild the trajectories from 12 pH-REMD .nc files named
> name.ph${X}.nc
> (where X ranges from 01 to 12). I have to say that I don't get cpptraj so
> much. Can anybody tell me the command to achieve this goal?
>
> Thank you in advance,
> Elisa
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--
Jason M. Swails
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Received on Wed Aug 24 2016 - 20:00:02 PDT
