[gmx-users] Periodic Molecules

[Lakshman Ji Verma]

Thanks Justin. A follow up question for my better understanding.

Does it mean that with “periodic-molecules” False, the periodic images
won’t affect interactions in the actual simulation box, whereas they will
affect if I keep “periodic-molecules” True?

Thanks
Lakshman

On Tue, May 29, 2018 at 10:53 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/29/18 11:50 AM, Lakshman Ji Verma wrote:
> > What difference it will make I keep Periodic molecules option True or
> False?
> > I read the manual but couldn’t understand more than keeping it False will
> > be faster.
>
> The "periodic-molecules" option is for use with "infinite" systems like
> CNT, surfaces, etc. That is, the topology specifies bonds that always
> span a periodic boundary. This option is distinct from normal PBC.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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