[gmx-users] CNT going outside during NVT

[Naga Rajesh Tummala]

It is better to freeze the atoms of nanotube and make sure the one of the
box dimension is same as the nanotube length (and the C-C bond length in
the nanotube across the PBC is right), so that you have infinitely long
nanotube.

If you want model flexible nanotube then you can unfreeze the atoms, but
make sure the force-field parameters are right.



On Thu, Mar 5, 2015 at 11:31 AM, soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Dear Justin,
>                  Thank u for your time. I would like to ask again about the
> problem I'm facing. From my understanding, If the DNA is supposed to wrap
> around the swCNT (i.e findings of other papers), should'nt I fix it inside
> the box? I have a box in the center of which the DNA is kept and the CNT is
> rather randomly placed along with the solvent molecules and ions. Do u
> prefer me to use freeze group to fix the position of CNT or are you saying
> that I should not worry about it since pbc is operative? Sorry I'm a newbie
> and this CNT modelling is something I am unfamiliar with..
>
>
> Regards,
> Soumadwip Ghosh
> IITB, Mumbai,
> India
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-- 
Naga Rajesh Tummala