From: Matthew Guberman-Pfeffer (matthew.guberman-pfeffer_at_yale.edu)
Date: Wed Sep 02 2020 - 01:01:25 CDT
Peter, thank you for your answer, particularly for telling me how I
could confirm the calculation was running correctly.
Best,
Matthew
On Tue, Sep 1, 2020 at 1:23 AM Peter Freddolino <petefred_at_umich.edu> wrote:
> 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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