[gmx-users] Possible trjconv malfunction?

[Nathan Scott]

Justin,

I actually must have mistyped that, the command below also fails with the
same error.

echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002  -e
20002 -o g96/stn_wt_a_1_0.g96 -novel

I will explore -dump though, thanks for the suggestion!

Best Wishes,
Nathan


On Thu, Jun 26, 2014 at 10:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/26/14, 10:02 AM, Nathan Scott wrote:
>
>> Hi all,
>>
>> I am trying to use trjconv to extract .g96 files iteratively, then use my
>> own software for analysis, then delete the .g96 file, but I am running
>> into
>> perplexing behavior. I did a bit of searching in the list archive but can
>> find no mention of this, so it could well be I am just doing something
>> wrong.
>>
>> I have a continuation (the original simulation was run for 20 ns) of a
>> simulation that was run for 50,000 steps, dt=0.002 ps, with the xtc file
>> written every 1000 steps (2 ps). When I issue the following command
>> everything works fine and I get a .g96 file ad the header shows a time of
>> 20000.
>>
>> echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20000 -e
>> 20000 -o g96/stn_wt_a_1_0.g96 -novel
>>
>> But when I try to extract the next file, which should be 2 ps later in the
>> simulation by using this command, I get an error:
>>
>> echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e
>> 20000 -o g96/stn_wt_a_1_0.g96 -novel
>>
>> WARNING no output, last frame read at t=20004
>>
>> When I run with -b and -e set to 20004 I get a .g96 file with a time of
>> 20004. I tried 20001, 20002, and 20003 just to see what happens, and I get
>> the same error referencing 20004 as the "last frame read."
>>
>> trjconv seems to think that there are 4 ps between frames. Just to check
>> myself, I did a gmxdump of the .xtc file and the .edr file, and they both
>> show a frame at 20002 ps and a final frame of the trajectory at 20100,
>> exactly as I expected, .Also, when I use trjconv -sep to output all of the
>> individual frames of the trajectory in one shot, I get 51 files with
>> correct timings in the headers, 20000, 20002, 20004, etc up to 20100.
>>
>> If anyone could shed light on this problem I would very much appreciate
>> it.
>> This is Gromacs 4.6.5, by the way, being run on Trestles at the SDSC
>> through an XSEDE account. I am running into problems trying to extract all
>> of the structure files at once to the per-node scratch space so I thought
>> I'd give iterative extraction a try, since my analysis code runs in serial
>> anyway.
>>
>>
> Your trjconv command is simply wrong.  You've specified -b 20002 -e 20000,
> so you're telling trjconv to start at a time that is after it has ended, so
> it chokes on the next frame (20004) because it can't satisfy the conditions
> you've set.  Using -b 20000 -e 20002 should be fine.  Note that -dump is
> much more efficient and circumvents similar problems.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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 | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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