Hi,
On Fri, Aug 11, 2017 at 3:36 PM, Aseel Bala <balaahme.msu.edu> wrote:
> However, I am running into an issue when 4 is on one edge of the frame and 5
> is on the other edge. In these situations, 4 is actually H-bonded to an
> 'image' of 5 produced by the periodic boundary condition. Let's call this
> image 5prime.
What you are describing is an imaging artifact, and is very common in
MD simulations with PBC and coordinate wrapping. The 'autoimage'
command was designed to handle this kind of situation. Instead of
'center' and 'image', try:
autoimage origin anchor :4
Hope this helps,
-Dan
PS - FYI the 'hbond' command in cpptraj now handles imaging natively
via the 'image' keyword.
>
>
>
> In this case, cpptraj actually centers 4 and 5 instead of 4 and 5prime.
>
>
>
> Is there a way that cpptraj can be used to center a molecule and the closest
> image of another molecule to it? So that I would be able to have 4 and
> 5prime in the center?
>
>
>
> Thank you very much in advance!
>
>
>
> --
>
>
>
> Aseel M. Bala
>
> Michigan State University
>
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sat Aug 12 2017 - 11:00:02 PDT
