[gmx-users] Problem with combining the .edr files
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Thu Mar 16 02:48:02 CET 2017
Thanks Mark :-)
Problem solved.
On Wed, Mar 15, 2017 at 1:10 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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