[gmx-users] Nanotube and DNA with periodic boundary conditions

Bob Johnson robertjo at physics.upenn.edu
Sun Aug 14 01:51:08 CEST 2005

Hello everyone,
I'm currently studying the interaction between an infinite carbon nanotube and a
single stranded DNA molecule. I am using the Amber force field for the DNA
molecule. I am building my system in XLeap and then converting the resulting
coordinate and topology file to the GROMACS format. However, the periodic
boundary conditions (to make the nanotube infinite) don't seem to work with
this topology (despite using pbc = full). It seems that to simulate an infinite
nanotube I must generate its topology with x2top and use the -pbc option. ONLY
when I generate the topology this way do I get a stable, infinite nanotube.
Assuming that this is true, this is how I've been proceeding.

1. Build system in Amber's XLeap

2. Convert coordinate and topology file to GROMACS format. This gives the files
gromos.g96 and gromacs.top

3. Copy the nanotube coordinates in gromos.g96 to a new file called cnt.g96

4. Generate the nanotube topology. This is the command I use:
x2top -f cnt.g96 -o cnt.top -pbc

5. Overwrite the old nanotube topology in gromacs.top with cnt.top. The topology
for the DNA, water, and ions remains unchanged.

6. Edit the box size in gromos.g96 such that the z-dimension of the box is equal
to the length of the nanotube plus a C-C bond length (so the images match up)

7. Run the simulation with pbc = full

The result is a mess. Pieces of the nanotube jump to the next image box and
cause the program to crash. I then tried giving the nanotube carbon atoms a
huge mass (so they wouldn't move). This prevented the jumping. However, the DNA
molecule was unstable (pieces moving around frantically) and some of its bonds
became too large and the simulation crashed.

Simulations of a single infinite nanotube generated from x2top -pbc produce a
stable structure. Also, simulations of the DNA generated from Amber produce
stable results. Only when I combine the two systems do I have problems. Is
there some incompatibility between the x2top topology and the topology
converted from Amber when I use pbc = full?

It seems that the problem is more than just an energetically unfavorable
configuration. I've tried many things to try to reduce that: making the
nanotube carbons more massive, running minimizations, reducing the temperature,
constraining the bonds. All of these provide either crashes or unstable results.

Does anybody know what the x2top -pbc option does and how it works with
pbc=full? If I knew that maybe I would have some insight into what's going on.
I'm really out of ideas here. If anyone could give me some suggestions I would
really appreciate it!
Thanks for you time,
Bob Johnson

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