On Mon, Apr 25, 2016 at 5:39 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Dear Amber users,
>
> I ran CpHMD silmuations in explicit solvent and pH replica exchange. Due to
> the waltime, I ran them splitting the simulations in two parts. So now I
> have trajectory files named
>
> traj.ph{X}.nc
> traj.phBIS{X}.nc
>
> where X spans from 01 to 12.
> I want to merge the two parts and then rebuild the trajectory file (i.e the
> snapshots) for each pH value. I made a few attempts with cpptraj, but I
> didn't get results. Do you know how to solve this?
>
trajin traj.pH1.nc trajnames traj.pH2.nc,traj.pH3.nc,traj.pH4.nc,...
trajin traj2.pH1.nc trajnames traj2.pH2.nc,traj2.pH3.nc,traj2.pH4.nc
,...
You need a separate trajin line for each "chunk", and you need to tell each
trajin line what all of the other trajectories were called for all other
replicas in your pH-REMD run.
HTH,
Jason
--
Jason M. Swails
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Received on Mon Apr 25 2016 - 03:30:05 PDT
