From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Sep 01 2020 - 00:23:26 CDT
Yes, the unit cell should be read from each frame of the dcd file if the
simulation was originally run with periodic boundary conditions. You should
be able to confirm this both from the presence of a message ("Updating unit
cell from timestep.") that will print after each call to `coorfile read`,
and from the fact that the VOLUME field of the output should fluctuate
accordingly.
Best,
Peter
On Tue, Sep 1, 2020 at 1:06 AM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer_at_yale.edu> wrote:
> Dear NAMD Listserve,
>
> When running a PairInteraction calculation over a trajectory, what is the
> correct way to specify the periodic boundaries? If I specify the cell
> vectors in the conf file, do the vectors get updated to reflect the cell
> fluctuations during the trajectory?
>
> Best regards,
> Matthew
>
>
>
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