- Posts: 7
Failed to run simulation
- lihie
- Topic Author
- Offline
- Fresh Boarder
I'm new in CG simulation, after running successfully em, the simulation crashes in pr. The system is a protein in a water box. The topology files were created using the martinize.py script. The system was properly minimized but now I'm, receiving the following error while running it on 8 nodes: "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = 1 2 4, box vector[2] = -nan -nan -nan"
And the following error while running it on 1 node: "Number of grid cells is zero. Probably the system and box collapsed."
I tried to run a new simulation with a different protein, and it all went well, so I guess I'm doing it ok.
If someone can help me I'll be more then thankful,
Lihie
Please Log in or Create an account to join the conversation.
- xavier
- Offline
- Admin
- Posts: 416
lihie wrote: Hello all,
I'm new in CG simulation, after running successfully em, the simulation crashes in pr. The system is a protein in a water box. The topology files were created using the martinize.py script. The system was properly minimized but now I'm, receiving the following error while running it on 8 nodes: "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = 1 2 4, box vector[2] = -nan -nan -nan"
And the following error while running it on 1 node: "Number of grid cells is zero. Probably the system and box collapsed."
I tried to run a new simulation with a different protein, and it all went well, so I guess I'm doing it ok.
If someone can help me I'll be more then thankful,
Lihie
Please Log in or Create an account to join the conversation.
- Clement
- Offline
- Admin
- Posts: 211
Run a:
Please Log in or Create an account to join the conversation.
- lihie
- Topic Author
- Offline
- Fresh Boarder
- Posts: 7
Thank you for replying. The box dimension appears in the gro file so this is not the problem. I read in the gromacs manual on grid and the way it calculates the atoms in the system and with xavier suggestion I tried to build different sizes of the box, and finally it worked.
Thank's again,
Lihie
Please Log in or Create an account to join the conversation.