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

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Sep 20 21:23:16 CEST 2015

Hi Soumadwip,

ssDNA or dsDNA? There are scripts for building both. I have one for ssDNA
that might be suitable for your purpose. You can contact me off-list if
you're interested.



On Sun, Sep 20, 2015 at 5:56 PM, soumadwip ghosh <soumadwipghosh at gmail.com>

> 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
> Mumbai
> India
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Tsjerk A. Wassenaar, Ph.D.

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