[gmx-users] concatenating 2 xtc files

[Kavyashree M]

Dear Sir,

First trajectory - traj1.xtc (0 to 5... ns)
Second trajectory -  traj2.xtc (5... to 25ns)

But there is no gap in between.
for concatenating -
$ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc

For nujump -
$ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc

I also have a case where I ran 10ns in 64 cores and later
continued in 8core machine. This also has the same problem.
While running in 64 cores by default it did not generate
the checkpoint file. So I has to use tpbconv to generate
a new tpr file for continuing from the same point  -

$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr

Thanks in advance.

Regards
Kavya




On Thu, Aug 1, 2013 at 12:20 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Kavya,
>
> That shouldn be a problem. Please post your sequence of commands for
> concatenating and further processing of the trajectory.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M <hmkvsri at gmail.com> wrote:
>
> > Dear users,
> >
> > I ran a simulation for 25ns. First 5ns in 8 core machine
> > and late part in 64 cores. It ran without any problem. The
> > trajectories were concatenated, jumps are removed and
> > rmsd was calculated. But there was sudden jump in the
> > rmsd curve. Is it wrong to run simulations in different
> > cores like this?
> >
> > Thank you
> > Regards
> > Kavya
> > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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