Visualize NAMD truncated octahedral box

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.

  1. 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

parm *.prmtop #load topology file based on AMBER force field.
trajin non_wrapped_box.dcd #load not wrapped trajectory file.
center :1-10 #assuing residue 1 to 10 is the center of box.
image center familiar #image the truncated octahedral box.
trajout wrapped_box.dcd dcd #output the wrapped box.

 

 

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