[gmx-users] (no subject)

[tarak karmakar]

Hi PAULAMI,

Use gmx trjcat to concatenate the two trajectory files and then calculate
the rmsd.
http://manual.gromacs.org/programs/gmx-trjcat.html

Best wishes,
Tarak

On Thu, Jul 9, 2015 at 1:34 PM, PAULAMI CHATTERJEE <
chatterjee_paulami at yahoo.co.in> wrote:

> Dear All,
> I have a 30 ns trajectory which I would like to extend up to 100 ns. For
> that I gave the following commands
> gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr
> gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append
> After completion of the extension two new trajectory files were generated-
> 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the
> trajectory with
> gmxcheck -f traj_comp.xtc
> the output is
> Checking file traj_comp.xtc
> Reading frame 0 time 30000.000
> # Atoms 16867
> Precision 0.001 (nm)
> Last frame 35000 time 100000.000
>
> This trajectory file contains coordinate values from 30ns to 100ns. I
> tried to calculate the rmsd with this file (both the trr and xtc file) but
> the graph abruptly starts from 30ns (instead of 0) and continues upto
> 100ns.For the calculation I need the total trajectory from time 0 to time
> 100ns.I think I am missing something.
> Can anyone please suggest anything here? Which one is the total trajectory
> file then?
> Thanks in advancePaulami
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.