[gmx-users] Inaccurate time frame

[Mark Abraham]

On 12/07/10, Hsin-Lin Chiang  <jiangsl at phys.sinica.edu.tw> wrote:
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>     Hi, Mark
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>     Thank you for your reply.
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>     I know -skip -sep is more robust.
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>     Since the definition talked about nr-th frame but not nr-th ps.
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>     -skip     int     1     Only write every nr-th frame
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>     -[no]sep     bool     no     Write each frame to a separate .gro,
>     .g96 or .pdb file
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>     The problem is that -skip 1000 -sep didn't consist of several time
>     frames in the same file but just write nr-th frame.
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>     That's why I use -split 1000 -timestep 1 according these definitions
>     found in manual.
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>     -split     time     0     Start writing new file when t MOD split =
>     first time (ps)
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>     -timestep     time     0     Change time step between input frames
>     (ps)
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>     With -dt it is possible to reduce the number of frames in
>     the output. This option relies on the accuracy of the times
>     in your input trajectory, so if these are inaccurate use the
>     -timestep option to modify the time (this can be done
>     simultaneously).
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>     Would you please teach how to use -skip -sep to get the same kind of
>     file which include all of 1000ps time frames together in a 1ns gro
>     file?
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Ah, sorry, I didn't read you well enough.

I've just seen that GROMACS 4.5 introduced trjconv -round to address this kind of issue. I suppose you will find trjconv -round -split works for you.

Mark


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>     I'll appreciate to any helps.
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>     Sincerely yours,
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>     Hsin-Lin
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> > >  Hi,
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> > > My time unit is 1ps and today I have 300ns data generated by parallel simulation.
> > > I use trjconv -split 1000 on my trajectory but get the truncated end at t= 5000.00000
> > > Theoretically it should stop at t= 1000.000
> > > I found that I don't have t= 1000.00000 frame but have t= 1000.00006, 2000.00012, 3000.00024, and t= 4000.00024.
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> > > I know I can add -timestep 1 to solve this problem and let file can be truncated at t= 1000.00006.
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> > > How does this kind of inaccurate time frames happen?
> > > Is this trajectory a wrong result?
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> > I just wrote a FAQ+wiki page for this, since it gets asked a bit. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
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> > trjconv -skip -sep is a more robust approach here
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> > Mark
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