[gmx-users] Problem with combining the .edr files
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 time0.000 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 time0.000 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 time0.000 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 4.000 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 8.000 Opened system_MD.5.edr.edr as single precision energy file Reading energy frame 0 time 12.000 Opened system_MD.5.part0003.edr.edr as single precision energy file Reading energy frame 0 time 32.000 Opened system_MD.5.part0004.edr.edr as single precision energy file Reading energy frame 0 time 57.000 Opened system_MD.5.part0005.edr.edr as single precision energy file Reading energy frame 0 time 82.000 Summary of files and start times used: FileStart time - NJOB_1.edr0.000 NJOB_2.edr0.000 NJOB_3.edr0.000 NJOB_4.edr4.000 NJOB_5.edr8.000 system_MD.5.edr.edr 12.000 system_MD.5.part0003.edr.edr 32.000 system_MD.5.part0004.edr.edr 57.000 system_MD.5.part0005.edr.edr 82.000 Opened NJOB_1.edr as single precision energy file Reading energy frame 0 time0.000 Continue writing frames from t=0, step=0 Last energy frame read 0 time0.000 Last step written from NJOB_1.edr: t 0, step 0 Opened NJOB_2.edr as single precision energy file Reading energy frame 1 time2.500 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=1 Last energy frame read 2000 time 4.000 Writing frame time 4 Last step written from NJOB_3.edr: t 4, step 2000 Opened NJOB_4.edr as single precision energy file Reading energy frame 1 time 40020.000 Continue writing frames from t=40020, step=2001 Last energy frame read 2000 time 8.000 Writing frame time 8 Last step written from NJOB_4.edr: t 8, step 4000 Opened NJOB_5.edr as single precision energy file Reading energy frame 1 time 80020.000 Continue writing frames from t=80020, step=4001 Last energy frame read 2000 time 12.000 Writing frame time 12 Last step written from NJOB_5.edr: t 12, step 6000 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=6001 Last energy frame read 1 time 32.000 riting frame time 32 Last step written from system_MD.5.edr.edr: t 32, step 16000 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=16001 Last energy frame read 12500 time 57.000 riting frame time 56 Last step written from system_MD.5.part0003.edr.edr: t 57, step 28500 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=28501 Last energy frame read 12500 time 82.000 riting frame time 82 Last step written from system_MD.5.part0004.edr.edr: t 82, step 41000 Opened system_MD.5.part0005.edr.edr as single precision energy file Reading energy frame 1 time 820020.00
Re: [gmx-users] Problem with combining the .edr files
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.moh...@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 time0.000 > 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 time0.000 > 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 time0.000 > 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 4.000 > 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 8.000 > Opened system_MD.5.edr.edr as single precision energy file > Reading energy frame 0 time 12.000 > Opened system_MD.5.part0003.edr.edr as single precision energy file > Reading energy frame 0 time 32.000 > Opened system_MD.5.part0004.edr.edr as single precision energy file > Reading energy frame 0 time 57.000 > Opened system_MD.5.part0005.edr.edr as single precision energy file > Reading energy frame 0 time 82.000 > > Summary of files and start times used: > > FileStart time > - >NJOB_1.edr0.000 >NJOB_2.edr0.000 >NJOB_3.edr0.000 >NJOB_4.edr4.000 >NJOB_5.edr8.000 > system_MD.5.edr.edr 12.000 > system_MD.5.part0003.edr.edr 32.000 > system_MD.5.part0004.edr.edr 57.000 > system_MD.5.part0005.edr.edr 82.000 > > Opened NJOB_1.edr as single precision energy file > Reading energy frame 0 time0.000 > Continue writing frames from t=0, step=0 > Last energy frame read 0 time0.000 > Last step written from NJOB_1.edr: t 0, step 0 > > Opened NJOB_2.edr as single precision energy file > Reading energy frame 1 time2.500 > 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=1 > Last energy frame read 2000 time 4.000 Writing frame time > 4 > Last step written from NJOB_3.edr: t 4, step 2000 > > Opened NJOB_4.edr as single precision energy file > Reading energy frame 1 time 40020.000 > Continue writing frames from t=40020, step=2001 > Last energy frame read 2000 time 8.000 Writing frame time > 8 > Last step written from NJOB_4.edr: t 8, step 4000 > > Opened NJOB_5.edr as single precision energy file > Reading energy frame 1 time 80020.000 > Continue writing frames from t=80020, step=4001 > Last energy frame read 2000 time 12.000 Writing frame time > 12 > Last step written from NJOB_5.edr: t 12, step 6000 > > 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=6001 > Last energy frame read 1 time 32.000 riting frame time > 3
Re: [gmx-users] Problem with combining the .edr files
Thanks Mark :-) Problem solved. On Wed, Mar 15, 2017 at 1:10 PM, Mark Abraham 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.moh...@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 time0.000 > > 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 time0.000 > > 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 time0.000 > > 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 4.000 > > 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 8.000 > > Opened system_MD.5.edr.edr as single precision energy file > > Reading energy frame 0 time 12.000 > > Opened system_MD.5.part0003.edr.edr as single precision energy file > > Reading energy frame 0 time 32.000 > > Opened system_MD.5.part0004.edr.edr as single precision energy file > > Reading energy frame 0 time 57.000 > > Opened system_MD.5.part0005.edr.edr as single precision energy file > > Reading energy frame 0 time 82.000 > > > > Summary of files and start times used: > > > > FileStart time > > - > >NJOB_1.edr0.000 > >NJOB_2.edr0.000 > >NJOB_3.edr0.000 > >NJOB_4.edr4.000 > >NJOB_5.edr8.000 > > system_MD.5.edr.edr 12.000 > > system_MD.5.part0003.edr.edr 32.000 > > system_MD.5.part0004.edr.edr 57.000 > > system_MD.5.part0005.edr.edr 82.000 > > > > Opened NJOB_1.edr as single precision energy file > > Reading energy frame 0 time0.000 > > Continue writing frames from t=0, step=0 > > Last energy frame read 0 time0.000 > > Last step written from NJOB_1.edr: t 0, step 0 > > > > Opened NJOB_2.edr as single precision energy file > > Reading energy frame 1 time2.500 > > 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=1 > > Last energy frame read 2000 time 4.000 Writing frame time > > 4 > > Last step written from NJOB_3.edr: t 4, step 2000 > > > > Opened NJOB_4.edr as single precision energy file > > Reading energy frame 1 time 40020.000 > > Continue writing frames from t=40020, step=2001 > > Last energy frame read 2000 time 8.000 Writing frame time > > 8 > > Last step written from NJOB_4.edr: t 8, step 4000 > > > > Opened NJOB_5.edr as single precision energy file > > Reading energy frame 1 time 80020.000 > > Continue writing frames from t=80020, step=4001 > > Last energy frame read 2000 time 12.000
