AMBER Archive (2006)

Subject: AMBER: imaging issue

From: David Smith (David.Smith_at_irb.hr)
Date: Sun Oct 29 2006 - 10:26:07 CST

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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