David-
Have you looked at file-imaged.bps with a trajectory viewing program (with
imaging turned off, if it is an option in the viewer), to see if it is a
problem with the way the file is being saved? It seems like the imaging is
working, but is not being saved in the trajout file so it's lost when you read
back in.
Kristina
Quoting David Smith <David.Smith.irb.hr>:
> Hi everyone,
>
> I'm having a bit of a problem with imaging coordinates obtained from a
> simulation with a truncated octahedron "box".
>
> Specifically, I have the situation which has been discussed many times
> on the reflector where I have two molecules that I would like to keep as
> close together as I can (I don't expect them to always be together but I
> would actually like to know how much they are together).
>
> I had been previously using a rectangular box and the standard solution
> like:
>
> trajin file.bps
> trajout file-imaged.bps binpos nobox
> center :1-15 mass origin
> image origin center
> center :1-30 mass origin
> image origin center
> distance d :1-15 :16-30 out d.dat
> strip :WAT
>
> had been working fine.
>
> Furthermore, and this is the key point for me, if I read in the
> trajectory with no water and no box (e.g. file-imaged.bps in the above
> script), and recalculated the distance between the two COMs, I would get
> exactly the same answer as from the above script.
>
> When I repeat the same procedure with a truncated-octahedron shaped unit
> cell, I am no longer able to get the same answer from the above script
> and a subsequent run from ptraj where I read in the imaged trajectory
> (with no water and no box).
>
> The problem I am having is independent of whether I use triclinic or
> familiar imaging (the latter with or without an additional COM mask),
> and whether or not I try to image bymol or byres or any other
> combination that I could come up with. For example, from reading the
> documentation, I would think that the following two scripts should give
> me the same distance:
>
> trajin file.bps
> trajout file-imaged.bps binpos nobox
> center :1-15 mass origin
> image origin center familiar com :1-15
> distance d :1-15 :16-30 out d-box.dat
> prnlev 4
>
> trajin file-imaged.bps
> distance d :1-15 :16-30 out d-nobox.dat
> prnlev 4
>
> However, they don't.
>
> For 1 particular frame, the first run tells me:
>
> DISTANCE: NON IMAGED is 65.724
> DISTANCE: 0 -1 0 is 18.950
>
> and d-box.dat rightly contains 18.950.
>
> In the second run, however, d-nobox.dat contains 65.724 as if the imaged
> trajectory has not been imaged at all.
>
> Am I misunderstanding what the imaging is meant to be doing or is
> something not working as it should?
>
> Any help would be appreciated.
>
> Thanks,
>
> David.
>
>
> --
> Dr. David Smith
> Division of Organic Chemistry and Biochemistry
> Rudjer Boskovic Institute
> Bijenicka 54
> 10002 Zagreb, Croatia
> tel: +385-1-4571252
> fax: +385-1-4561118
>
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--
Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556
(574)631-3904
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Received on Wed Nov 01 2006 - 06:07:18 PST
