[gmx-users] Removing periodic boundary conditions using trjconv

David spoel at xray.bmc.uu.se
Thu Aug 18 20:29:20 CEST 2005

On Thu, 2005-08-18 at 12:40 -0400, Bob Johnson wrote:
> Hello everyone,
> I'm simulating the interactions between single stranded DNA and an infinite
> carbon nanotube. I finally got the simulations to work (thank you David and
> everyone else for your input). The DNA adsorbs to the nanotube pretty quickly
> but wanders around  along the surface of the tube. It's seems that it maintains
> a fixed radial distance from the tube center but moves along the z (tube axis)
> and the phi (tube circumference) directions. Sometimes the DNA slides into the
> next periodic box in the z direction.
> When I view the trajectory in VMD, a portion of the DNA moves to the right and
> goes into the next box. Of course, because of periodic boundary conditions, an
> exact replica of this portion is then shifted back into the box. However, VMD
> tries to draw bonds between the DNA and the portion that has been shifted.
> Thus, long bonds are drawn across the nanotube's length. I was playing around
> with trjconv to see if I could suppress the periodic boundary conditions for
> the purpose of visualization. I've used all the different -pbc options already
> and none of them helped. Any suggestions on how to go about doing this? In the
> end, it may be a problem with how VMD represents a trajectory.

You can probably center the trajectory on the DNA using trjconv.

> Thanks,
> Bob Johnson
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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