AMBER Archive (2009)

Subject: [AMBER] ptraj imaging of namd generated trajectories

From: Vlad Cojocaru (
Date: Thu Aug 13 2009 - 04:35:49 CDT

Dear AMBER users,

I performed some simulations with NAMD using the AMBER force field and a
Leap-generated truncated octahedron.
NAMD transforms the box into an equivalent triclinic box defined by a
3x3 matrix .

Now, I tried to analyze these trajectories using ptraj (AmberTools
1.2)... However, it seems that ptraj is not able to correctly image the
center :1-492 mass origin
image origin center familiar (or image origin center triclinic)

builds a strange cubic box (with gaps along the 3 axes) although in the
ptraj output its written that the box is an "exact truncated octahedron".
Now I thought that this might be because ptraj reads the box info from
the topology file where the box dimension is larger than in the final
state (box shrank during equilibration).
So, I tried to define "box" command in ptraj but I think this works only
with cubic boxes .. Is that right ?

I saw this question on the archive but no answer to it. I thought
somebody might know the trick to get back the truncated octahedron from
a NAMD generated trajectory

Best wishes

Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533202 Fax: ++49-6221-533298


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