Re: dcd files

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 22 2011 - 09:15:48 CDT

On Sun, May 22, 2011 at 9:24 AM, PAUL NEWMAN <paulclizana_at_gmail.com> wrote:

> Yes I support this post.
>

actually, converting binary data to ascii only to read it back and parse it
(i.e. convert it back to binary) is something i would not call a smart idea.
better to deal with the binary data directly.

>
> Can anyone provide C routines to read the binary files for positions and
> velocity; so that we can incorporate them into our programs to calculate
> other properties.
>
>
several options exist. for example, VMD contains the molfile plugin library
which has a uniform API to read in a large variety of file formats. using
such
a library is hugely preferential to writing your own, since file formats in
MD are almost always ad hoc formats and rarely well documented.
on top of that, a lot of programs that implement well documented formats,
e.g. PDB, don't produce standard conforming files, as the authors
often didn't read the standard or were not careful programmers.

> Or at least what is the format of these files (positions and velocity) so
> they can be read.
>
>
the documentation for the DCD format are the CHARMm sources.

cheers,
     axel.

Thanks
>
>
> On Sun, May 22, 2011 at 9:02 AM, Molecular Dynamics <
> moleculardynamics_at_yahoo.com> wrote:
>
>> Dear namd users,
>>
>> Is there a tool for converting binary dcd files into ascii format in order
>> to do analysis for dynamic properties ?
>>
>> Thanks in advance
>>
>> M
>>
>
>
>
> --
> Cheers,
>
> Paul
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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