AMBER Archive (2009)

Subject: [AMBER] Re: ptraj imaging of namd generated trajectories

From: Vlad Cojocaru (
Date: Thu Aug 13 2009 - 05:10:54 CDT

Dear Ambers,

So I have a fix to my problem. Maybe its useful for others as well ..
Here is ptraj input that correctly recreates the truncated octahedron

trajin traj.dcd
box x 99.0077 y 99.077 z 99.077 alpha 109.471221 beta 109.471221 gamma
109.471221 fixx fixy fixz fixalpha fixbeta fixgamma
center :1-492 mass origin
image origin center familiar
trajout traj.cdf netcdf

The trick is the box command (which does work for other shapes than
cubic). Crucial is the use of "fixx fixy fixz fixalpha fixbeta
fixgamma". This overrides what it is read from the dcd trajectory.
Apparently the box info from the dcd trajectory is not read correctly.

Best wishes

Vlad Cojocaru wrote:
> 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

Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

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


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