Re: dcd files

From: PAUL NEWMAN (paulclizana_at_gmail.com)
Date: Sun May 22 2011 - 14:46:57 CDT

Hello Everyone,

What is the format for the DCD trajectory file for position and velocity.
If possible, Can someone provide a simple pseudocode? for reading trajectory
files?

On Sun, May 22, 2011 at 3:38 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> A NAMD binary file (restart/output, not DCD trajectory) consists of the
> atom count as a 32-bit integer followed by all three position or velocity
> components for each atom as 64-bit double-precision floating point, i.e.,
> NXYZXYZXYZXYZ... where N is a 4-byte int and X, Y, and Z are 8-byte doubles.
> If the number of atoms the file contains is known then the atom count can be
> used to determine endianness.
>
> The VMD molfile plugins are the best source of file I/O code examples.
>
> -Jim
>
>
> On Sun, 22 May 2011, PAUL NEWMAN wrote:
>
> Yes I support this post.
>>
>> 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.
>>
>> Or at least what is the format of these files (positions and velocity) so
>> they can be read.
>>
>> 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
>>
>>

-- 
Cheers,
Paul

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