Is it possible to continue simulation in the same file by -noappend option?

[JakubH]

GROMACS version: 2018.4
GROMACS modification: No
Hi, I have questions. I hope yuo will help me.

1. In the past I used -append when I run the simulation. For example:
   First I prepared .tpr file
   gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
   Then I run a simulation
   gmx mdrun -deffnm eq1 -v
   Then for example I stop simulation by ctrl+C and run my simulation again
   gmx mdrun -deffnm eq1 -cpi eq1.cpt -append -v - so my trajectory and energies was add to my eq1.edr and eq1.xtc files

Now I have a bigger system and I need to use -noappend, because I will transfer my files quite often. For example, I will make new files (part1,part2 etc) every 100 ns.
So ok the beginning is the same
gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
gmx mdrun -deffnm eq1 -v
then I changed in my mdp file number of steps 100mln -> 200 mln
ok so I change them and I run my simulation
gmx grompp -f eq4.mdp (in .mdp file I change number of steps) -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
then I use -noappend
gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
so I will get files like eq1.part0002.edr/trr/xtc
but for example my simulation will stop at 150 mln, because I use ctrl+C or there is a problem with clusters etc.
But when I run
gmx mdrun -deffnm eq1 -cpi eq1.cpt -noappend -v
It will create another files eq1.part0003.edr/trr/xtcfrom 150 to 200 mln steps instead of adding to files eq1.part0002.edr/trr/xtc
Is it possible to continue to writing in the same file by -noappend option?

2. and I have also a question about backing up my files - is it enough to keep checkpoints files or I should better have a copy of all my files (it will be hard because I would need a lot of space).
3. Is it true that a sudden power cut can damage my .edr and trajectory files? Because last time my .edr file was damaged but my disk was good and I had enough space, so maybe a power cut could damage my simulation when I continue them on the next day?

Thank you in advance
Jakub

[alevilla]

Hi,
In general, If your run generates very large files, you can consider to tune the save frequency for xtc edr and log files according your needs, and if you need to generate a trr file and which information you need to have in trr file (position, velocity, force). See mdp option for output control

@JakubH

1. In the past I used -append when I run the simulation. For example:
   First I prepared .tpr file
   gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
   Then I run a simulation
   gmx mdrun -deffnm eq1 -v
   Then for example I stop simulation by ctrl+C and run my simulation again
   gmx mdrun -deffnm eq1 -cpi eq1.cpt -append -v - so my trajectory and energies was add to my eq1.edr and eq1.xtc files
   Now I have a bigger system and I need to use -noappend, because I will transfer my files quite often. For example, I will make new files (part1,part2 etc) every 100 ns.
   So ok the beginning is the same
   gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
   gmx mdrun -deffnm eq1 -v
   then I changed in my mdp file number of steps 100mln → 200 mln
   ok so I change them and I run my simulation
   gmx grompp -f eq4.mdp (in .mdp file I change number of steps) -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
   then I use -noappend
   gmx grompp -f eq4.mdp -c eq2_333temp.gro -r eq2_333temp.gro -p system.top -o eq1.tpr
   so I will get files like eq1.part0002.edr/trr/xtc
   but for example my simulation will stop at 150 mln, because I use ctrl+C or there is a problem with clusters etc.
   But when I run
   gmx mdrun -deffnm eq1 -cpi eq1.cpt -noappend -v
   It will create another files eq1.part0003.edr/trr/xtcfrom 150 to 200 mln steps instead of adding to files eq1.part0002.edr/trr/xtc
   Is it possible to continue to writing in the same file by -noappend option?

No

2. and I have also a question about backing up my files - is it enough to keep checkpoints files or I should better have a copy of all my files (it will be hard because I would need a lot of space).

checkpoint file has the information of the last frame. Thus it depends on which information you need to save.

3. Is it true that a sudden power cut can damage my .edr and trajectory files? Because last time my .edr file was damaged but my disk was good and I had enough space, so maybe a power cut could damage my simulation when I continue them on the next day?

if the power cut occurs in the moment the files are saved, the files are damaged. You can recover the last frame information from the checkpoint file (if it is not damaged)

You can find some help also here
http://manual.gromacs.org/current/user-guide/managing-simulations.html

Best regards
Alessandra