There is no file of em.gro after energy minimization

User discussions
1

GROMACS version: recent version
GROMACS modification: No
Here post your question

Hello. I try to Gromacs tutorial using a Lysozyme example. But I have a big problem.
When I did minimization, but there are no em.gro file in my folder.

like this:

D:\Gromacs_in_windows\New>gmx mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, 2024.1 (-:

Executable: C:\gmx-install\bin\gmx.exe
Data prefix: C:\gmx-install
Working dir: D:\Gromacs_in_windows\New
Command line:
gmx mdrun -v -deffnm em

Back Off! I just backed up em.log to ./#em.log.1#
Reading file em.tpr, VERSION 2024.1 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads

Back Off! I just backed up em.trr to ./#em.trr.1#

Back Off! I just backed up em.edr to ./#em.edr.1#

Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000

D:\Gromacs_in_windows\New>

and there is a one file which is em.trr but the file volume is 0 KB.

What should I do?

Please tell me anything about this issue.

Thank you.

1 Like
2

What compiler did you use to compile GROMACS? I wonder if it’s related to Calculations do not start after launching gmx mdrun (#4956) · Issues · GROMACS / GROMACS · GitLab, even if it’s not exactly the same.

3

Thank you so much about your reply.

I’m using Microsoft Visual C++ 2015-2022 Redistributalbe now.

4

em.log (16.6 KB)
em.mdp (1.1 KB)

5

Thank you so much about your reply.

I’m using Microsoft Visual C++ 2015-2022 Redistributalbe now.

6

Would you be able to recompile it with, e.g., g++/gcc? It would be interesting to see if that helps. Hopefully there will be a fix for this soon.

7

Hello! Thanks to you, I’ve solved the problem. I really appreciate it. Have a great day!

8

Great to hear! Could you explain what you did that solved it? That might help others with the same problem.

9

I tried downloading and using Gromacs on the Windows command prompt, but you mentioned a compile bug. So, I had no choice but to proceed with Ubuntu, and I was able to proceed without any issues. If you hadn’t mentioned it, I would have struggled all day trying to resolve it. Thanks again for your help.