I am running MD analysis for the self-assembly of collagen. Upon the analysis for Radius of Gyration, we observed that the simulation box size isn't adequately large enough. I am extending the simulation runs for additional time period, and wanted to see if there was a way i can increase the simulation box size, without having to start over again.
I think it is not possible to introduce any changes once you have started the MD run. I tried myself many times to change the total timestep for extended run while the program is already running but it does not execute the command until and unless you stop and restart it again.
Dear Atul Rawal,
unfortunately if you believe the box is small, you will need to simulate everything again, in my opinion. MD is very dependent on the initial state.
Once you define the boundaries of you calculation, all cutoffs in energy and length of interactions are already take into account. To change all of them, you need to stop, change and restart.
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running