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
trajectories
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
Vlad
--
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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Received on Wed Aug 19 2009 - 22:21:01 PDT
