Re: calculation of periodic box

From: Michael Thomas (exploding.dinosaurs_at_gmail.com)
Date: Tue Nov 17 2009 - 22:56:55 CST

What I meant to ask is, throughout the simulation the periodic box
vectors can change (in response to constant pressure control). How does
NAMD work out these new vectors? If it is defined by the minmax(x,y,z),
then in a periodic system does NAMD choose to wrap a molecule around to
the other side of the system?

Roman Petrenko wrote:
> NAMD doesn't ! You indicate it in the config file.
>
> cellBasisVector1 Ax Ay Az
> ...
> ...
> cellOrigin
>
>
> or if you use restart, it is written in the *.xsc files produced by
> NAMD after the first run.
>
>
> On Tue, Nov 17, 2009 at 11:16 PM, Michael Thomas
> <exploding.dinosaurs_at_gmail.com> wrote:
>
>> Hi everyone,
>>
>> How does NAMD calculate the size of the periodic box during the simulation?
>> Where exactly do the numbers for the box's vectors in the xst file come
>> from?
>>
>> Thanks,
>>
>> Michael
>>
>>
>>
>
>
>
>

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