GROMACS version: 2024
GROMACS modification: No
em.log (16.5 KB)
its stoping at
Reading file em.tpr, VERSION 2024 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Are you running on Windows? It sounds similar to No run after gmx mdrun, also filed in No run after gmx mdrun (#4956) · Issues · GROMACS / GROMACS · GitLab. If so, could you test if the error still occurs if you run with the option -nb cpu?
Sorry, I checked the log file and saw that you are running on Windows, and also with the -nb cpu option. I’ll update the issue report with that information.
Yes I tried both -nb option as well as without. Yes we are running it on windows. I think if you could fix this issue it will be useful to a lot of student researchers as windows is used mostly used by students. Is this bug fixable , if it is when do you expect to finish it?
It should definitely be fixable, and as you say, it might affect many people. So, it has a high priority. We hope to have it fixed in 2024.2, which should be released in two months.
Nice sir it will help a lot of people . And maybe can lead to integration of many gui to help assist a lot of people which will lead to lot of citations .
Hi @muzammilkabier , thanks for the report.
Could you share the tpr file you used and the command lines executed to compile GROMACS?
Does it happen also on a regular simulation?
I will give those files within tommorow.
The command line I used to build is given below. I didnt get what you meant about regular simulation.
Thanks.
Could you recompile GROMACS with “-DCMAKE_BUILD_TYPE=Debug” and see if the bug still occurs?
What I meant about regular simulation is a molecular dynamics simulation like a small equilibration.
I will try and inform you
I only tried with simulation like as per tutorials on gromacs protein ligand webpage
i tried compilin with debug and it didnt work it showed an error at this command “gmx pdb2gmx -f protein.pdb -o protien.gro -water spc -ff charmm36-jul2021”
error which occurred and the tpr file is given below.
(Attachment em.tpr is missing)
i tried compiling with debug and it didn’t work it showed an error at this command “gmx pdb2gmx -f protein.pdb -o protien.gro -water spc -ff charmm36-jul2021” the error was showing debug assertion failed.
The tpr file is given below.
(Attachment em.tpr is missing)
Thanks.
You don’t need to redo the whole procedure with the Debug binary, just the minimization (gmx mdrun -v -deffnm em -nb cpu) with the tpr you previously obtained (although the pdb2gmx should not fail like this, I’ll take a look).
The tpr was not uploaded also.
i tried compiling with debug and it didn’t work it showed an error at this command “gmx pdb2gmx -f protein.pdb -o protien.gro -water spc -ff charmm36-jul2021” the error was showing debug assertion failed.
The tpr file is given below.
Gromacs is not allowing tor attachment
Ok I have given Google drive link to tpr and let me check just that command
hey minimization is working with debug
Thanks for the response.
We’ll invistigate it and post follow up here: Calculations do not start after launching gmx mdrun (#4956) · Issues · GROMACS / GROMACS · GitLab
em.tpr