Dear Justin, this is my trjcat command
/home/cocktail/vitalini/gromacs_special/bin/trjcat -f /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_annealing.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_annealing2.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_min.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_min1.gro -o /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_traj_tot.xtc -settime -cat I'm using the settime command to have each structure at a different time step. If I was using it wrongly please correct me. Thanks in advance for all the help. Francesca 2012/6/16 Justin A. Lemkul <jalem...@vt.edu> > > > On 6/16/12 6:48 AM, francesca vitalini wrote: > >> Dear Gromacs Users, >> >> While making a trajectory connecting different gro files I got the >> following >> output which I don't understand. >> >> Continue writing frames from >> /home/cocktail2/vitalini/**reverse_transformation_vacuum/** >> 300-166-160/300-166-160_**annealing.gro >> t=1 ps, frame=0 >> Last frame 0 time 0.000 >> WARNING: Frames around t=1.000000 ps have a different spacing than the >> rest, >> might be a gap or overlap that couldn't be corrected automatically. >> Reading frames from gro file 'Protein', 15230 atoms. >> Reading frame 0 time 0.000 >> WARNING: Couldn't find a time in the frame. >> >> Can anyone explain to me the implication of this warning message? >> >> > Trajectories need time information, .gro files don't have any. In the > absence of your trjcat command, I can only assume you're not using -settime > to specify what time point to which each frame corresponds. If that's not > the case, please provide the command you are using. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412
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