[gmx-users] To trjcat or not to trjcat
nedomacho at gmail.com
Thu Dec 15 22:25:34 CET 2016
I have implemented what Justin suggested -- works perfectly fine (thanks
Justin!). I am very bad at bash scripting, but this was simple even for me.
However, what you are suggesting may become extremely useful later on, both
in terms of using trjcat and dealing with repeated back-to-back frames. I
just keep using GMX what it absolutely was not designed to do, hence the
weird scenarios. One day I will hire a LAMMPS-wielding postdoc. One day. :)
On Thu, Dec 15, 2016 at 1:51 PM, Mark Abraham <mark.j.abraham at gmail.com>
> You wanted automatic, which Justin's sequence achieves via writing a
> script. But you can render trjcat non-interactive and that might be easier.
> See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
> Probably you can make your life even easier in future by judicious use of
> init-time in the mdp files for your "restarts."
> On Fri, 16 Dec 2016 02:14 Alex <nedomacho at gmail.com> wrote:
> > Since the first frame of trajectory (N+1) will be the same as the last
> > frame of trajectory N, then you need to do two things:
> > >
> > > 1. Use trjconv -b 50 to remove the first frame from all but the first
> > > trajectory. This eliminates the duplicate frames.
> > > 2. Then use trjconv -t0 to set a new start time for each trajectory.
> > > This is easily done as part of a loop in a shell script.
> > > 3. trjcat
> > > 4. Profit?
> > >
> > > -Justin
> > >
> > This sounds like exactly what I wanted, thank you!
> > --
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