[gmx-users] initial structure generation for performing MD simulations

[soumadwip ghosh]

Hi all,
       Is there any way to insert a 12 nt DNA inside a 15x15 single
wall carbon nanotube using some scripts in VMD or some tools like
Packmol? I want to study the displacement of nucleic acids from the
core of a CNT at different conditions (temperature, solvent or
incrporation of fillers). Can anyone suggest me a way to build up my
initial structure or do I have to run a short simulation to achieve
the same (ref. Gao et al. 2006. Nano Letters)?

Thanks for your time in advance

Soumadwip Ghosh
Research Fellow
IITB
Mumbai
India