Re: dcd files

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun May 22 2011 - 14:53:45 CDT

The format of DCD files is only simple in FORTRAN, so you really do need
to look at the VMD molfile plugins. The units of velocities and forces
are described in the "File formats" section of the NAMD User's Guide.

-Jim

On Sun, 22 May 2011, PAUL NEWMAN wrote:

> 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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