From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jul 10 2012 - 12:25:08 CDT
I'm not sure about this - it seems NAMD does some pretty smart things to avoid such violations: http://www.ks.uiuc.edu/Research/namd/2.9/ug/node39.html
See the outputPairlists option.
On Jul 10, 2012, at 5:24 AM, Axel Kohlmeyer wrote:
> On Tue, Jul 10, 2012 at 1:44 AM, Thomas Brian <thomasbrianxlii_at_gmail.com> wrote:
>> Hi namd-l,
>>
>> If an atom enters another atoms cutoff without being in its pairlist, what
>> error/warning, if any is displayed in the output file?
>
> no. such a test would *kill* performance.
> it is up to the user, to choose reasonable
> settings, so that this does not happen.
>
>> Also, does namd back up and redo the last "cycle" number of timesteps? (I
>
> no.
>
>> saw somewhere that pairlist violations do not affect the dynamics and I
>> don't know how that would be possible unless namd backed up and redid
>> calculations)
>
> well, if you are missing interactions due to too infrequent pairlist rebuilds
> to too small a cutoff for it, then you *do* miss those interactions. if this is
> infrequent, however, you may not notice. whether this is a good or bad
> thing, is a different discussion.
>
> axel.
>
>> Thanks,
>> Tom
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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