Re: Periodic molecules in NAMD

From: Vermaas, Joshua (
Date: Wed Dec 13 2017 - 12:18:31 CST

Hi Bogdan,

Yes. Bonds across the periodic boundary are what is typically done for
cellulose or other polymers that you want to make infinite. Since the
distances computed are always PBC correct, this doesn't actually need
anything all that special, unlike in CHARMM.


On 12/13/2017 04:20 AM, Bogdan MAREKHA wrote:
> Dear NAMD community,
> I am wondering if it would be possible with NAMD to simulate an
> 'infinite' molecule that spans across PBC, for example a carbon nanotube
> or a stretched polymer chain?
> I know that there are such tools within Gromacs, the question is then
> are there any ways of doing something similar within NAMD?
> Regards,
> Bogdan

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