Periodic boundary condition

From: Weitao Wang (weitaowa_at_andrew.cmu.edu)
Date: Wed Sep 11 2019 - 16:08:05 CDT

Hi NAMD users,

I'm trying to apply periodic boundary condition to a DNA origami tube. My
purpose is to make it a long tube in one dimension. I have two quetions.

1. I used the following to define my periodic box, which was measured in
VMD:
*"cellOrigin -0.00375375640578568 -0.00027379687526263297
-0.001771773211658001*
*cellBasisVector1 43.9799995422 0 0*
*cellBasisVector2 0 20.9799995422 0*
*cellBasisVector3 0 0 216.618003845"*
But the dcd file showed the tube was not continuous when I visualized it in
VMD and drew periodic images. I was wondering which part went wrong.

2. If I add extra bonds between atoms at two borders of the box(the most
left and most right side), the tube still was not continuous. I thought in
this case, the extra interaction should happen between two nearest tubes,
rather than in the same tube where the distance between two atoms is very
long and bond length is also very long.

Thanks for your time.

Best,
Weitao

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