[gmx-users] Problem with combining the .edr files

[Mohsen Ramezanpour]

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 ...*