Re: Get number of timesteps from DCD via script

From: Axel Kohlmeyer (
Date: Wed Feb 09 2011 - 08:43:21 CST

> 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.


Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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