[gmx-users] concatenating 2 xtc files

[Kavyashree M]

Sir,

Thank you for the suggestion.. I will make use of it in
future runs. but now the simulation is over.

There was some overlap of few ns in 8core machine.
so while checking the rmsd plot there was a significant
difference in rmsd between 8 core and 64 core overlapped
region of simulation.

1 more question is suppose I do not have checkpoint file
and if I need to continue from a stopped point (not extending)
does this command do the job?
$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr

Because when I tried with this there was a jump in the rmsd

Thank you
Regards
Kavya



On Thu, Aug 1, 2013 at 5:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/1/13 3:42 AM, Kavyashree M wrote:
>
>> 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
>>
>>
> I would suggest using gmxdump on new.tpr to verify that the coordinates it
> contains are the same as the last frame in traj.trr.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>