[gmx-users] trjcat error of different spacing
Justin A. Lemkul
jalemkul at vt.edu
Thu May 5 16:37:41 CEST 2011
Anirban Ghosh wrote:
> 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?
>
Run gmxcheck on all your trajectories. It is possible that something (very)
early on is not matching with something much later. The flat line you reported
in the g_sas output indicates that the problem may not be at 3000000 ns, but
rather around 10 ns. What that problem is exactly is hard to say at this point,
but you may have a corrupted frame somewhere in that interval that's throwing
things off.
-Justin
> Thanks,
>
> Anirban
>
> On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> 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
>
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--
========================================
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
========================================
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