On 06/22/2012 05:19 PM, Daniel Roe wrote:
> Hi,
>
> On Fri, Jun 22, 2012 at 11:07 AM, Jan-Philip Gehrcke
> <jgehrcke.googlemail.com> wrote:
>> As stated in the AmberTools 1.5 manual, cpptraj by default applies the
>> 'image' procedure before calculating the distance. In my case, the two
>> atoms in question definitely did not move out of the primary box,
>
> The manual is a little misleading on this point. It is more accurate
> to say that "the minimum-image convention is used", i.e. the shortest
> distance is always used by default unless 'noimage' is specified.
This explains the issue. Thanks for the clarification, Daniel!
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Received on Mon Jun 25 2012 - 03:00:02 PDT
