[gmx-users] trjcat error of different spacing

[Anirban Ghosh]

Hello Justin,

I am using Gromacs 4.0.7
Actually, I am joining around 20 trajectories of around 300 ns each. Its a
CGMD run. But I reported here only those two trajectories between which
trjcat has shown the warning while joining.
So what should i do?

Thanks,

Anirban

On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Anirban Ghosh wrote:
>
>> Hello Justin,
>>
>> Thanks for the reply.
>> gmxcheck on the first trajectory shows:
>>
>>
>> -------------------------------------------------------------------------------------------------
>> Checking file protein_3000NS_2.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame       0 time 2957280.000  # Atoms  57296
>> Reading frame    1400 time 2999280.000
>> Item        #frames Timestep (ps)
>> Step          1425    30
>> Time          1425    30
>> Lambda        1425    30
>> Coords        1425    30
>> Velocities    1425    30
>> Forces           0
>> Box           1425    30
>>
>> ---------------------------------------------------------------------------------------------------
>>
>> And on the second trajectory shows:
>>
>>
>> ---------------------------------------------------------------------------------------------------
>> Checking file B2AR_self_assembly_3500NS.trr
>> trn version: GMX_trn_file (single precision)
>> Reading frame       0 time 3000000.000  # Atoms  57296
>> Reading frame   16000 time 3480000.000
>> Item        #frames Timestep (ps)
>> Step         16667    30
>> Time         16667    30
>> Lambda       16667    30
>> Coords       16667    30
>> Velocities   16667    30
>> Forces           0
>> Box          16667    30
>>
>> ---------------------------------------------------------------------------------------------------
>>
>> So gmxcheck does not show any warning/error.
>> Then why I am getting the warning from trjcat. And how to remove it?
>>
>>
> I don't know yet.  A few more questions:
>
> 1. What version of Gromacs are you using?
>
> 2. How many total trajectories are you concatenating?  You said there was a
> problem from 10 -> 3000000 ns, but I don't see any times shown here below
> 2957280.  The real problem could be early on in the trajectory.
>
> -Justin
>
>  Thanks,
>>
>> Anirban
>>
>>
>> On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Anirban Ghosh wrote:
>>
>>
>>        Hi ALL,
>>
>>        I am trying to use trjcat -f input files -o output_file to join
>>        to very larger trajectories. However I am getting the following
>>        error:
>>
>>
>>  -------------------------------------------------------------------------------------------------------------------------------------------
>>        Continue writing frames from protein_3000NS_2.trr t=2.95728e+06
>>        ps, frame=98576      ->  frame 100000 time 3000000.000 ps     ->
>>         frame  99980 time 2999400.000 ps    WARNING: Frames around
>>        t=3000000.000000 ps have a different spacing than the rest,
>>        might be a gap or overlap that couldn't be corrected automatically.
>>        Reading frame       0 time 3999990.000  lasttime 3e+06
>>
>>        Continue writing frames from protein_4000NS.trr t=3.99999e+06
>>        ps, frame=100001
>>  -------------------------------------------------------------------------------------------------------------------------------------------
>>
>>        And if I use this resultant output trajectory for further
>>        analysis like g_sas, then a portion between around 10 ns and
>>        3000000 ns is simply joined by a straight line.
>>        How to remove this inconsistency from the two trajectories?
>>        Any suggestion is welcome.
>>
>>
>>    What does gmxcheck tell you about each of the individual
>>    trajectories (prior to running trjcat)?
>>
>>    -Justin
>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    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
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110505/a8f8963e/attachment.html>