[gmx-users] Possible trjconv malfunction?

[Christopher Neale]

Just a follow-up, since the -dump option is working for you. I have also found that -b 100 -e 100 sometimes doesn't work even where there is clearly a frame at 100 ps. I presume that this happens when there is a bit of a rounding issue in the simulation trajectory and the time is actually stored as 99.99999999 ps, so -b 100 doesn't catch it.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nathan Scott <scottjn at gmail.com>
Sent: 26 June 2014 16:49
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Possible trjconv malfunction?

Hi Chris,

It turns out that was a typo on my part, the error occurs when both -b and
-e values are set to a time that does exist in the trajectory file. -dump
seems to be working great, and thanks for the tip on including -b as well
to speed up trjconv!

Best Wishes,
Nathan


On Thu, Jun 26, 2014 at 1:12 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> You listed:
>
> 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
>
> And your -b value is less than your -e value, so you should not get any
> output, which is what happens.
>
> Try using -dump to extract a single frame. If you want, you can also
> supply -b with the -b value slightly less than the -dump value (since this
> will make trjconv run faster).
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nathan
> Scott <scottjn at gmail.com>
> Sent: 26 June 2014 10:05
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Possible trjconv malfunction?
>
> 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.
>
> Thanks in advance for any help!
>
> Best Wishes,
> Nathan
>
> PS My apologies if this came through twice, it appears to me that I sent to
> the wrong email address (gmx-users at gromacs.org) the first time around.
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