I tried to generate my continuation file from 4500 using tpbconv. Any reason the shouldn't work? Do I need to truncate the trr file specifically?




In message <44C51F84.5090809@xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users@gromacs.org> writes:
> Samantha Kaye wrote:
> > But the first file can't be successfully gmxcheck-ed, I get the precision error mentioned below.
> ok, I see. You will have to truncate it after 4500 ps using trjconv -e 
> or trjconv -trunc
> 
> > 
> > 
> > In message <44C504B8.2040101@xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users@gromacs.org> writes:
> > 
> >>Samantha Kaye wrote:
> >>
> >>>Yes using trjcat. It returns a magic number error.
> >>
> >>could this by chance be run on a 64 bit powerpc?
> >>
> >>If the two original files can be gmxcheck-ed then the catted file should 
> >>be fine too.
> >>
> >>
> >>>
> >>>In message <44C4CA58.5080209@xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users@gromacs.org> writes:
> >>>
> >>>
> >>>>Samantha Kaye wrote:
> >>>>
> >>>>
> >>>>>Hi,
> >>>>>
> >>>>>Whenever I try to make a continuation file for my simulation I can generate a tpr file using tpbconv but I can't cat the ouput files together afterwards.
> >>>>>
> >>>>
> >>>>did you use trjcat ?
> >>>>
> >>>>
> >>>>
> >>>>>When I run ">gmxcheck -f closed1122_unrest.trr" on the first trr file I get the following:
> >>>>>
> >>>>>
> >>>>>Checking file closed1122_unrest.trr
> >>>>>trn version: GMX_trn_file (single precision)
> >>>>>Reading frame       0 time    0.000
> >>>>># Atoms  189376
> >>>>>Reading frame     910 time 4550.000   -------------------------------------------------------
> >>>>>Program gmxcheck, VERSION 3.3
> >>>>>Source code file: trnio.c, line: 66
> >>>>>
> >>>>>File input/output error:
> >>>>>Can not determine precision of trn file
> >>>>>-------------------------------------------------------
> >>>>>
> >>>>>
> >>>>>I've tried generating the continuation file from an earlier frame but have the same problem always at frame 910.
> >>>>>
> >>>>>The file is over 2gb but as tpbconv runs without a problem I don't think that's the problem.
> >>>>>
> >>>>>Any suggestions?
> >>>>>
> >>>>>Thanks
> >>>>>
> >>>>
> >>>>
> >>>>-- 
> >>>>David.
> >>>>________________________________________________________________________
> >>>>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >>>>Dept. of Cell and Molecular Biology, Uppsala University.
> >>>>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> >>>>phone:	46 18 471 4205		fax: 46 18 511 755
> >>>>spoel@xray.bmc.uu.se	spoel@gromacs.org   http://folding.bmc.uu.se
> >>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>_______________________________________________
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> >>>
> >>>
> >>
> >>-- 
> >>David.
> >>________________________________________________________________________
> >>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >>Dept. of Cell and Molecular Biology, Uppsala University.
> >>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> >>phone:	46 18 471 4205		fax: 46 18 511 755
> >>spoel@xray.bmc.uu.se	spoel@gromacs.org   http://folding.bmc.uu.se
> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>_______________________________________________
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> >>
> > 
> > 
> 
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel@xray.bmc.uu.se	spoel@gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
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> 

-- 
Samantha Kaye
Structural Bioinformatics and Computational Biochemistry Group
University of Oxford