[gmx-developers] format of tpr file

[Roland Schulz]

On Thu, May 23, 2013 at 12:12 PM, Zhuyi Xue <alfred532008 at gmail.com> wrote:
> I am writing a tpr parser in Python for MDAnalysis, so curious about it.
>
> I have already written one for parsing tpr files of version tpx 58 and 73
> using the Python module xdrlib, which follows  RFC 1014.
>
> Using the gromacs library is possibly a better idea, but I am still not sure
> of how to compile it alone and then call it from Python. The disadvantage is
> that in that case, MDAnalysis will need to depend on Gromacs.

There are already several python gromacs bindings:
http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/alternatives.html,
https://github.com/GromPy/GromPy . But as far as I know there is none
which is up-to-date with gromacs 4.6. It would be great if we had
something official in the gromacs code so that it stays up to date.
Let us know if you would be interested in contributing to it. The
dependency issue we solved the following way for VMD in Gromacs.
Gromacs checks at runtime whether VMD is available. That way one can
compile Gromacs without VMD but if VMD is available it can be used
(for reading non-Gromacs file types).

Roland

>
> Does that mean the XDR version doesn't matter?
>
> Zhuyi
>
>
> On Thu, May 23, 2013 at 11:58 AM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>>
>> On 2013-05-23 17:54, Zhuyi Xue wrote:
>>>
>>> Hi, there,
>>>
>>> I am wondering which version of XDR does tpr file strictly follow. Is it
>>> RFC 1014  in 1987 (http://tools.ietf.org/html/rfc1014) or RFC 1832 in
>>> 1995 (http://www.ietf.org/rfc/rfc1832.txt), or it just doesn't matter?
>>>
>>> Thank you,
>>> Zhuyi
>>>
>>>
>> Why do you care?
>>
>> If you try to read it yourself you are wasting your time. You can just
>> link to the gromacs library.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>
>



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