AMBER Archive (2005)

Subject: AMBER: distance between images

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Wed Jan 05 2005 - 04:34:46 CST

Dear AMBER users,

I would like to analyse the minimum distance between my solute and its
images
during my simulation. I am working with an octahedron box of solvent.
I did not find anything in the AMBER package to do this. All I can do is
to use ptraj
to create all the neighbours of my solute and then to look at it with
VMD (as proposed
by Dr Cheatham in the mailing list in 2004). But this cannot be done for
all my snapshots of the trajectories
because because of the time it takes do do it....
I saw that there is a possibility to do such a thing in the gromacs
package (g_mindist) that can read
AMBER trajectory files but there is a problem when one uses an
octahedron box because the way
the box is written in AMBER trajectory file does not correspond to what
is done in old gromos file.

Does anyone know if there is an "easy" way to look at distance between
images for a whole trajectory ?

Thank you in advance for your answers,
Sincerely yours,
Fabien 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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