[gmx-users] Problem with combining the .edr files
Mark Abraham
mark.j.abraham at gmail.com
Wed Mar 15 20:10:42 CET 2017
Hi,
Judging from your start times, you're concatenating apples with oranges :-)
In this case, probably NVT equilibration with NPT production, or similar.
Arguably, concatenating the trr files in that case is also conceptually
wrong, even if the file format is not robust enough to hint that you're
trying to do something that will leave you with a file whose contents have
an interpretation that is somewhere between unclear and wrong. edr is
actually smart enough to perhaps stop you doing something that isn't useful.
Mark
On Wed, Mar 15, 2017 at 7:26 PM Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:
> Dear Gromacs users,
>
> I did a simulation in parts using -noappend command, so I have a few .trr
> and .edr files which I wish to merge.
>
> I have difficulty with that and I could not find any related post on that
> except this one:
> http://comments.gmane.org/gmane.science.biology.gromacs.user/68806
>
> Using Gromacs 2016.2 installed on my PC (without MPI), and the following
> command:
> gmx trjcat -f *.trr -o fixed.trr
> I will have a reasonable .trr file. However, when I use:
>
> gmx eneconv -f *.edr -o fixed.edr
>
> I get the followings:
> ============================================
> Opened NJOB_1.edr as single precision energy file
> Last energy frame read 0 time 0.000
> Opened NJOB_2.edr as single precision energy file
> Energy files don't match, different number of energies:
> NJOB_1.edr: 55
> NJOB_2.edr: 55
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame 0 time 0.000
> Opened NJOB_3.edr as single precision energy file
> Energy files don't match, different number of energies:
> NJOB_2.edr: 55
> NJOB_3.edr: 58
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame 0 time 0.000
> Opened NJOB_4.edr as single precision energy file
> Energy files don't match, different number of energies:
> NJOB_3.edr: 58
> NJOB_4.edr: 57
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame 0 time 40000.000
> Opened NJOB_5.edr as single precision energy file
> Energy files don't match, different number of energies:
> NJOB_4.edr: 57
> NJOB_5.edr: 60
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame 0 time 80000.000
> Opened system_MD.5.edr.edr as single precision energy file
> Reading energy frame 0 time 120000.000
> Opened system_MD.5.part0003.edr.edr as single precision energy file
> Reading energy frame 0 time 320000.000
> Opened system_MD.5.part0004.edr.edr as single precision energy file
> Reading energy frame 0 time 570000.000
> Opened system_MD.5.part0005.edr.edr as single precision energy file
> Reading energy frame 0 time 820000.000
>
> Summary of files and start times used:
>
> File Start time
> -----------------------------------------
> NJOB_1.edr 0.000
> NJOB_2.edr 0.000
> NJOB_3.edr 0.000
> NJOB_4.edr 40000.000
> NJOB_5.edr 80000.000
> system_MD.5.edr.edr 120000.000
> system_MD.5.part0003.edr.edr 320000.000
> system_MD.5.part0004.edr.edr 570000.000
> system_MD.5.part0005.edr.edr 820000.000
>
> Opened NJOB_1.edr as single precision energy file
> Reading energy frame 0 time 0.000
> Continue writing frames from t=0, step=0
> Last energy frame read 0 time 0.000
> Last step written from NJOB_1.edr: t 0, step 0
>
> Opened NJOB_2.edr as single precision energy file
> Reading energy frame 1 time 2.500
> Last step written from NJOB_2.edr: t 0, step 0
>
> Opened NJOB_3.edr as single precision energy file
> Reading energy frame 1 time 20.000
> Continue writing frames from t=20, step=10000
> Last energy frame read 2000 time 40000.000 Writing frame time
> 40000
> Last step written from NJOB_3.edr: t 40000, step 20000000
>
> Opened NJOB_4.edr as single precision energy file
> Reading energy frame 1 time 40020.000
> Continue writing frames from t=40020, step=20010000
> Last energy frame read 2000 time 80000.000 Writing frame time
> 80000
> Last step written from NJOB_4.edr: t 80000, step 40000000
>
> Opened NJOB_5.edr as single precision energy file
> Reading energy frame 1 time 80020.000
> Continue writing frames from t=80020, step=40010000
> Last energy frame read 2000 time 120000.000 Writing frame time
> 120000
> Last step written from NJOB_5.edr: t 120000, step 60000000
>
> Opened system_MD.5.edr.edr as single precision energy file
> Reading energy frame 1 time 120020.000
> Continue writing frames from t=120020, step=60010000
> Last energy frame read 10000 time 320000.000 riting frame time
> 320000
> Last step written from system_MD.5.edr.edr: t 320000, step 160000000
>
> Opened system_MD.5.part0003.edr.edr as single precision energy file
> Reading energy frame 1 time 320020.000
> Continue writing frames from t=320020, step=160010000
> Last energy frame read 12500 time 570000.000 riting frame time
> 560000
> Last step written from system_MD.5.part0003.edr.edr: t 570000, step
> 285000000
>
> Opened system_MD.5.part0004.edr.edr as single precision energy file
> Reading energy frame 1 time 570020.000
> Continue writing frames from t=570020, step=285010000
> Last energy frame read 12500 time 820000.000 riting frame time
> 820000
> Last step written from system_MD.5.part0004.edr.edr: t 820000, step
> 410000000
>
> Opened system_MD.5.part0005.edr.edr as single precision energy file
> Reading energy frame 1 time 820020.000
> Continue writing frames from t=820020, step=410010000
> Last energy frame read 12352 time 1067040.000 riting frame time
> 1.06e+06
> Last step written from system_MD.5.part0005.edr.edr: t 1.06704e+06, step
> 533520000
>
> Last frame written was at step 533520000, time 1067040.000000
> Wrote 53353 frames
>
>
> ===================================================
> I will have a fixed.edr but 1) I am not sure if this is correctly merged,
> and 2) there is no option like T, kinetic energy, box size, ... in
> fixed.edr file when I use:
> gmx energy -f fixed.edr -o T.xvg
>
> This means the fixed.edr has problem.
>
> Since simulations were done on HPC with Gromcs version 4.6.7, I tried the
> same command with both eneconv and eneconv_mpi , but both failed too. This
> probably suggest that the problem is not what Mark suggested in previous
> discussion:
> http://comments.gmane.org/gmane.science.biology.gromacs.user/68806
>
> Any idea is appreciated in advance.
>
> Cheers
> Mohsen
> --
> *Rewards work better than punishment ...*
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