Tutorial 2 KALP15 in DPPC at http://www.mdtutorials.com/gmx/index.html

User discussions
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1

GROMACS version: gromacs/2022.1
GROMACS modification: No

I tried to run Tutorial 2 KALP15 in DPPC at GROMACS Tutorials. But, When prompting a command which is

gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr

there is an error message saying there is no nvt.gro or nvt.cpt files.
I think that its previous prompts are

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr -maxwarn 1
gmx mdrun -deffnm nvt

, and they did not generate nvt.gro and nvt.cpt. Is there anybody to encounter a similar problem and solve it by modifying the prompts?

Thanks in advance.

2

Did the simulation finish? Those are normal outputs produced by GROMACS at the end of the run. Try adding the -v flag and see how much time you have to wait, something like gmx mdrun -v -deffnm nvt. If you do not have the files then the first thing to debug is to find out if you are letting the simulation run or not!

3

1
I tried again adding -v and the message is attached. I am not sure if the simulation ended, but still there is no generation of nvt.gro and nvt.cpt.

Thanks.

4

You can see that the simulation was killed. Did you kill it? Do you have any idea about what process may have killed it?

The simulation is not completing so you are not getting any .gro/.cpt output files from it.

5

I do not have any idea since I just followed the TUTORIAL at KALP-15 in DPPC. It is not the codes I made, I am sorry.

6

What I mean is: does the killing happen automatically? Where are you running the simulations? it seems very weird that the process get automatically killed. What does the .log file of the simulations say?