Re: how to find cellorigin for periodic boundary condition

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 04 2012 - 10:37:47 CST

On Tue, Dec 4, 2012 at 5:34 PM, Maria Saeed <mariyasaeed_at_yahoo.com> wrote:
>
> Hi all,
>
> i have a query regarding membrane protein simulation
>
>
> How to calculate cell origin for boundary periodic conditions implemented
> for NAMD minimization script for simulation?
> what is the best way to find out the cell origin?

MD with periodic boundaries is invariant to translation,
i.e. the choice of the cell origin is arbitrary. it only
matters to writing out wrapped coordinates, where
the origin provides a reference point for the wrapping.

in other words, you choose an origin that is convenient
for visualization or analysis, but it doesn't matter much
beyond that (and you can always unwrap and wrap
after the fact, if you'd prefer to have a different origin).

axel.

>
>
> # Periodic Boundary Conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {1} {
> cellBasisVector1 77. 0. 0.
> cellBasisVector2 0. 77. 0.
> cellBasisVector3 0. 0. 90.
> cellOrigin 0.285711854696 0.299352765083 6.22171497345
>
> what is the formula of calculate cell origin and what is the best awy to
> find this value.
>
> if anybody know then plz guide me i will appreciate
>
>
> - -
> Regards,
>
> Maria Saeed.
>
>
>

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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