[gmx-users] trjcat xtc files

[Paymon Pirzadeh]

Apparently you are right! But my desktop has 4GB RAM, and to be honest,
when I load normal trajectories (I know they are smaller in size) but I
have not seen such issue in almost 60% increase in RAM occupation by
VMD. Normally I load 1000 frames, and now I want 3000 frames. Why should
it run to such a strange problem? 


On Mon, 2009-11-02 at 18:57 +0100, XAvier Periole wrote:
> 
> On Nov 2, 2009, at 18:13, Paymon Pirzadeh <ppirzade at ucalgary.ca> wrote:
> 
> > 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!
> Memory limit?
> >
> > 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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> >>
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