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

David spoel at xray.bmc.uu.se
Sun Aug 14 09:28:37 CEST 2005

On Sat, 2005-08-13 at 19:51 -0400, Bob Johnson wrote:
> 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.
What I'd do is the following. 
Build the nanotube topology using x2top, and run it in vacuo in a large
box to ensure it is stable. Build the DNA topology however you want,
merge the two topologies using a text editor and merge the coordinates
too. This is the crucial step. Take care that there is plenty of space
between DNA and nanotube. Do energy minimization and short posres
simulation with force constant 1000 (not 1e9 as this will cause high
frequency vibration which will make the system unstable).

Then add water using genbox and do posres simulation where you allow the
box axes perpendicular to the nanotube to fluctuate but not the one in
the direction of the tube.

Then you should be ready for production.
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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