NAMD to CHARMM unit cell information in DCD

From: François Marchand (
Date: Tue Oct 30 2007 - 14:29:41 CDT

Dear All,

I simulated several systems with NAMD-2.5 (CPT conditions) and I want to
analyze the trajectories with CHARMM, and specifically I would like to reset
the correct cell dimensions.

The problem is that I forgot to set the 'DCDUnitCell' option to 'yes', and
according to
( )
the default option in NAMD-2.5 is 'no'.

My question is: are the cell informations coded somewhere in the NAMD-dcd's or
are they definitively lost (what I expect...)?

If yes, how can I recover them in CHARMM format?

I tried 'catdcd' and
'dcdcellfix' (
(they set the cell dimension to 1.00 for every frame) and numerous CHARMM
scripts, but always unsuccessful thus far!

Thanks in advance for an answer!


François Marchand
Department of Biochemistry, Caflisch Group
University of Zurich, Winterthurerstrasse 190
CH-8057 Zuerich / Switzerland
 Phone  +41 1 635 55 59
 Fax      +41 1 635 68 62

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