Re: Get number of timesteps from DCD via script

From: Bjoern Olausson (
Date: Thu Feb 10 2011 - 03:52:44 CST

On Wednesday 09 February 2011 15:43:21 Axel Kohlmeyer wrote:
> > Thanks, that was informative!
> > For now I would be happy to figure out the proper header layout for NAMD
> > 2.7 64-bit compiled with ICC 11.1.046 (ELF 64-bit LSB executable, AMD
> > x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses
> > shared libs), for GNU/Linux 2.6.9) which only runs on one cluster.
> in that case, you have to worry much less. you will have 32-bit
> record-length markers and 32-bit integers. using the namd c-code
> as a reference is the best starting point, only you have to pay
> attention to the part that outputs the cell dimensions. you can
> tell from the value in the record-length marker, whether it is present
> or not. namd 2.7 should by default output the "new" dcd format that
> includes the cell dimensions and tilt (in some unusual order and
> angles as cosines). if you cannot find the info you need, i would
> suggest to look up the remaining details in the VMD dcd molfile plugin.
> also you should study which of the header entries NAMD actually
> does update and in what units.

Sounds like a plan!
Thanks a lot for the hints!


Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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