[gmx-users] trjcat xtc files

[Paymon Pirzadeh]

Hi Tom,
Thanks for the tip. It worked on the command line and I had 3000 frames.
But when I fed the file to VMD, it showed only 1800 frames!? Although
the initial and final configurations looked correct. I still am not sure
what possibly goes wrong!?

Payman


On Mon, 2009-11-02 at 10:50 +0000, TJ Piggot wrote:
> You should use the -settime option, I think it should solve your problem.
> 
> Tom
> 
> --On Monday, November 02, 2009 00:21:31 -0800 Payman Pirzadeh 
> <ppirzade at ucalgary.ca> wrote:
> 
> > Your second guess is correct! I used grompp to restart (I had thought it
> > might provide me with the chance to change things if needed). I was
> > surprised initially when "cat" command did not work! The number of frames
> > were most of the time less than what it should be.
> > I also checked the 'trjcat -h'. I did not specifically understand how I
> > might be able to get over this issue. Any advices?
> >
> > Payman
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> > On Behalf Of Mark Abraham
> > Sent: Sunday, November 01, 2009 8:37 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] trjcat xtc files
> >
> > Paymon Pirzadeh wrote:
> >> Sorry,
> >> My command line was:
> >>
> >>  trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc
> >> AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc
> >> AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o
> >> AFPI_Ih1010_54_58_Npt265_merged2-6.xtc
> >>
> >> the "_d_mpi" is the suffix used for double precision and parallel
> >> version of the installed gromacs.
> >
> > OK so now we have some idea what you might be trying to do. The most
> > likely causes are that the first few trajectories have no frames, or
> > that each frame in the earlier trajectories is common to one in the last
> > trajectory. This might happen if you were using grompp to do restarts,
> > or have previously assigned duplicate times somehow. If so, find a
> > better workflow in future. Consult trjcat -h for clues on how to get
> > around this.
> >
> > Mark
> >
> >> Payman
> >>
> >> On Mon, 2009-11-02 at 15:08 +1100, Mark Abraham wrote:
> >>> Paymon Pirzadeh wrote:
> >>>> Hello,
> >>>> I am trying to concatenate several xtc files. When I use the trjcat, it
> >>>> only writes the last file into the output file! where the problem could
> >>>> be?
> >>> In your command line. Why didn't you tell us what it was? :-)
> >>>
> >>> Mark
> >>> _______________________________________________
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> >>
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> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> 
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