Hi,
On Sat, May 18, 2019 at 3:46 PM Karolina Mitusińska (Markowska)
<markowska.kar.gmail.com> wrote:
>
> Ok, so... can I somehow add the information about number of frames/time
> into the NetCDF fle?
Yes, as of this morning. I just added a new command to the GitHub
version of cpptraj called 'time', which allows you to add, modify, or
remove time information from trajectory frames.
[help time]
{time0 <initial time> dt <step> [update] | remove}
Add, modify, or remove time information from each frame.
time0 <initial time> : Time of the first frame (ps).
dt <step> : Time step between frames (ps).
update : If specified, modify any existing time info.
remove : Remove any time info from frame.
So to add time data to a NetCDF file with the first frame starting at
10 ps and using a 2 fs time step:
parm myparm.parm7
trajin mytraj.nc
time time0 10 dt 0.002
trajout mytraj.time.nc
Hope this helps,
-Dan
>
> Best regards
> Karolina
>
> pt., 17 maj 2019 o 16:25 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
>
> > Hi,
> >
> > On Wed, May 15, 2019 at 2:13 PM Karolina Mitusińska (Markowska)
> > <markowska.kar.gmail.com> wrote:
> > > Now when I use Amber18/AmberTools18 to preprocess files (for example to
> > > skip some frames) I'm getting errors that my trajectory file does not
> > > contain informations about the time/timestep.
> >
> > So cpptraj didn't really handle time info in NetCDF files well in past
> > versions - in some cases I think the time information was silently
> > removed :-(. More recent versions of cpptraj (including I believe AT
> > 18) behave properly, i.e. they keep all information in the input
> > trajectory unless directed otherwise. The more recent versions of
> > cpptraj will also let you know if the time information is missing. You
> > can also quickly check if your NetCDF trajectory contains time info by
> > doing 'ncdump -h <file>' and checking for the existence of the
> > 'time(frame)' variable.
> >
> > Hope this clears things up (and apologies to all for old cpptraj's bad
> > behavior),
> >
> > -Dan
> >
> > >
> > > Did something change? And most important: how to make cpptraj to include
> > > such information into the trajectory file?
> > >
> > > Looking forward to help from you.
> > > Best regards
> > > Karolina Mitusińska
> > > PhD student
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Received on Mon May 20 2019 - 11:30:02 PDT
