I am using NAMD to run MD simulation with AMBER force field in a truncated octahedral box. To correctly image the box, you can do in following two ways. I use a long time to figure this out.
- Add “wrapall on” and “wrapnearest on” in NAMD configuration file, the generated DCD file will be in a good truncated octahedral box.
But I don’t like a wrapped box in the simulation. Some calculation need a not wrapped box like self-diffusion coefficient calculation. In this condition, DCD file will looks like a sphere in VMD. And you can not get a correct truncated octahedral box with “pbc wrap” command. You can solve this problem in the following way.
2. using Cpptraj in AMBERTOOLS. Set a center, and then image the system. A example input script is below