On Tue, Jul 8, 2014 at 7:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, Jul 6, 2014 at 3:20 AM, Mele N. <nm10g13.soton.ac.uk> wrote:
>
> > follow what you advice and run my analysis with AmberTools14 and
> > everything work fine. I also add on the top of each run trajectory a fake
> > line the first trajectory run. I don't really know where was the
> problem. I
> > am a bit confused on the reason why it doesn't work with Amber13Tools.
> >
>
> It seems like your trajectories do not have a title line (see
> http://ambermd.org/formats.html#trajectory for details). I think this can
> happen if you are running with the '-A' command line flag but no trajectory
> exists.
>
>
> > Are you using ASCII or NetCDF trajectories?
> >
> > I use ASCII trajectories,
> >
>
> I highly recommend switching to NetCDF trajectories (ioutfm=1). They have
> higher precision, are faster to process, and are far less error-prone than
> ASCII trajectories. I also recommend NetCDF restarts (ntxo=2).
>
In a redundant email, I'll strongly echo Dan's suggestion for NetCDF
trajectories. For everything I've ever done, they have only advantages
over ASCII (the one advantage Dan omitted is that NetCDF trajectories are
quite a bit smaller than ASCII trajectories unless the ASCII ones are
compressed with gzip or bzip2).
The NetCDF restarts also have many advantages. But they can't (yet) be
read into VMD and have fewer disadvantages to NetCDF restarts compared to
the trajectory comparison.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 08 2014 - 21:30:02 PDT
