WARNING: Incomplete energy frame: nr 1390086 time 1042563.750

JakubH · September 4, 2020, 12:22pm

GROMACS version: 2018.4
GROMACS modification: No
I have a problem. I run the membrane simulation. I continue my simulation if it stopped (for example lack of electricity) by using
gmx grompp -f eq4.mdp -p system_mgdg.top -c eq2_333temp.tpr -o eq2_333temp.tpr
then
gmx mdrun -deffnm eq2_333temp -cpi eq2_333temp.cpt -v -append

But my .edr file is damaged probably. I have 950000 steps and 1425 ns, not 1042 ns and 650000 steps.
I have also information
WARNING: Incomplete energy frame: nr 1390086 time 1042563.750

Statistics over 695042001 steps [ 0.0000 through 1042563.0000 ps ], 1 data sets
All statistics are over 6950421 points
What I should do now? Complete simulation? Run new simulation? Is it possiblethat only 1390086 is incomplete and the next frames are ok for example 1390087? How can I get these frames? Is it possible to generate edr file from trajectory?

cblau · September 4, 2020, 2:07pm

Hi Jakub,

I would say it depends on what data of your simulation you want to analyse and what type of output you saved.

it seems that up to the 1042 ns, things went fine and I would say that the data is usable.
if you don’t need to have a look at specific energy terms in your analysis and your .xtc looks fine, then continuing from the checkpoint file is okay, even if your energy file is corrupted in one frame
you can get back some information on the energies (an .edr file) by running gmx mdrun -rerun, (more information here: http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html), but this will never give you the full information, anything velocity related like kinetic energy you’ll miss.

JakubH · September 6, 2020, 1:02pm

First of all, thank you so much for response.

But what I should do if I want to have .edr file with information after 1042 ns? I think about three options.

Make a gro file from a .xtc/.trr file at 1042 ns and run another simulation, then use gmx eneconv and concatenate these two files.
Another good option could be a continuation by noappend option from 1042 ns. But I see that it is impossible to make a checkpoint file at specific time and without checkpoint, I can’t do this. GROMACS can only append to files when restarting from a checkpoint.
In older version of gromacs I can use gmx convert-tpr to read in .trr files (as they also keep track of velocity) with the -time option to produce new .tpr files that will produce an exact continuation of your trajectory from the specified time mark. But I use 2018.4 and I can’t see time option :(

cblau · September 7, 2020, 1:34pm

Hi Jakub,

I would go for continuing the simulation at 1042 ns using gmx grompp -time to create a new tpr file from your trr, then concatenate the output energy files and coordiantes.

JakubH · September 7, 2020, 1:35pm

Thanks a lot. This could be the best option. Thank you so much for you help.

JakubH · September 22, 2020, 12:21pm

Hi I have a problem
I use gmx grompp like you said
gmx grompp -f eq4.mdp -c eq1.tpr -t eq1.trr -p system_mgdg.top -o eq1_test20000.tpr -time 20000
:-) GROMACS - gmx grompp, 2018.4 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2018.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/jakub/Maxtor/MGDG_reversed_20_08_2019_real_wazne/testowanie_wznawiania
Command line:
  gmx grompp -f eq4.mdp -c eq1.tpr -t eq1.trr -p system_mgdg.top -o eq1_test20000.tpr -time 20000

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'

NOTE 1 [file eq4.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.


NOTE 2 [file eq4.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 3 [file eq4.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Setting the LD random seed to 856319666
Generated 190 of the 190 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 190 of the 190 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'mgdg'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Reading file eq1.tpr, VERSION 2018.4 (single precision)
Reading file eq1.tpr, VERSION 2018.4 (single precision)
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:  3600      Other residues
There are: 20385      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group Water is 122309.09
Number of degrees of freedom in T-Coupling group non-Water is 281697.91
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 333 K
Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read till time 20000
trr version: GMX_trn_file (single precision)
Reading frame     900 time 6750.000   
Using frame at t = 7312.5 ps
Starting time for run is 0 ps
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x216x120, spacing 0.099 0.097 0.100
Estimate for the relative computational load of the PME mesh part: 0.33

NOTE 4 [file eq4.mdp]:
  This run will generate roughly 2384127 Mb of data


There were 4 notes

Back Off! I just backed up eq1_test20000.tpr to ./#eq1_test20000.tpr.2#

GROMACS reminds you: "If you're doing I/O, you're doing it wrong!" (Cannada "Drew" Lewis)

Then I use mdun
gmx mdrun -s eq1_test20000.tpr -v
:-) GROMACS - gmx mdrun, 2018.4 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  
  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   
 Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    
  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  
  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   
    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  
   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2018.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/jakub/Maxtor/MGDG_reversed_20_08_2019_real_wazne/testowanie_wznawiania
Command line:
  gmx mdrun -s eq1_test20000.tpr -v


Back Off! I just backed up md.log to ./#md.log.5#
Reading file eq1_test20000.tpr, VERSION 2018.4 (single precision)
Changing nstlist from 5 to 100, rlist from 1 to 1.072

Using 1 MPI thread
Using 6 OpenMP threads 

1 GPU auto-selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
  PP:0

Back Off! I just backed up traj_comp.xtc to ./#traj_comp.xtc.5#

Back Off! I just backed up traj.trr to ./#traj.trr.5#

Back Off! I just backed up ener.edr to ./#ener.edr.5#

WARNING: This run will generate roughly 2380540 Mb of data

starting mdrun '900 mgdg molecules in water'
950000000 steps, 1425000.0 ps.
step  200: timed with pme grid 72 216 120, coulomb cutoff 1.000: 10233.0 M-cycles
step  400: timed with pme grid 64 192 108, coulomb cutoff 1.115: 7055.7 M-cycles
step  600: timed with pme grid 60 168 96, coulomb cutoff 1.252: 7836.8 M-cycles
step  800: timed with pme grid 52 160 84, coulomb cutoff 1.424: 7934.8 M-cycles
step 1000: timed with pme grid 52 160 96, coulomb cutoff 1.372: 8851.6 M-cycles
step 1200: timed with pme grid 56 160 96, coulomb cutoff 1.315: 6408.9 M-cycles
step 1400: timed with pme grid 56 168 96, coulomb cutoff 1.274: 6194.4 M-cycles
step 1600: timed with pme grid 60 192 100, coulomb cutoff 1.196: 6370.8 M-cycles
step 1800: timed with pme grid 64 192 104, coulomb cutoff 1.150: 6817.6 M-cycles
step 2000: timed with pme grid 72 192 112, coulomb cutoff 1.096: 8886.3 M-cycles
step 2200: timed with pme grid 72 200 112, coulomb cutoff 1.068: 8830.1 M-cycles
step 2400: timed with pme grid 72 200 120, coulomb cutoff 1.052: 8824.9 M-cycles
step 2600: timed with pme grid 72 208 120, coulomb cutoff 1.011: 10486.3 M-cycles
              optimal pme grid 56 168 96, coulomb cutoff 1.274
step 3400, will finish Fri Jun 25 09:58:13 2021

Ang I have a question, why this starts from the beginning? Is it ok. So its starts from the beginning (step 200), but in real it starts from 20000 yes?

cblau · September 25, 2020, 4:13pm

Hi Jakub,

You’re almost right - if you have a look at the grompp output, it seems like your simulation contains only frames up to 7.312 ns and not until 20 ns, that’s why grompp just takes the last frame and then starts the time-accounting at zero again. If I remember correctly, grompp should be able to set also the start time to continue your simulation at the “right” time, see grompp -h for that.

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WARNING: Incomplete energy frame: nr 1390086 time 1042563.750

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