[gmx-users] read trr file

[Tsjerk Wassenaar]

Hi Patrick,

Please find the code for reading TRR files attached. The neatest bit is
that it doesn't read the coordinates/velocities/forces for a frame, unless
you want them. That allows to do a quick indexing of frames first. The
offset argument to the TRR reader allows jumping to a specific (frame)
position.

If you have any issues or suggestions, please let me know. I'd also be
interested to hear about cool things that are achieved with the code :)

Cheers,

Tsjerk

On Wed, Nov 26, 2014 at 8:58 PM, Patrick Fuchs <
patrick.fuchs at univ-paris-diderot.fr> wrote:

> Thanks Tsjerk, I'm interested in having a routine that needs as less
> external library as possible. Pure python and numpy is perfect.
> Best,
>
> Patrick
>
> Le 26/11/2014 18:15, Tsjerk Wassenaar a écrit :
>
>  Hi Patrick,
>>
>> TRR files are rather simple in structure and are quite easy to parse with
>> pure python/numpy. That's not the case for XTC files.
>>
>> I'll make a few changes to the TRR reader, polishing a bit, and send it.
>> Probably next week, as I'll be occupied this weekend.
>>
>> Cheers,
>>
>> Tsjerk
>> On Nov 26, 2014 6:05 PM, "Patrick Fuchs" <
>> patrick.fuchs at univ-paris-diderot.fr> wrote:
>>
>>  Hi Tsjerk,
>>> I would be very interested by your python code. Does it also read xtc
>>> files? Shall I contact you off-list? Thanks.
>>> Best,
>>>
>>> Patrick
>>>
>>> Le 26/11/2014 06:26, Tsjerk Wassenaar a écrit :
>>>
>>>  I also have Python code to read TRR files directly. Contact me if you're
>>>> interested.
>>>>
>>>> Cheers,
>>>>
>>>> Tsjerk
>>>> On Nov 26, 2014 5:44 AM, "RINU KHATTRI" <nickname.mittu at gmail.com>
>>>> wrote:
>>>>
>>>>   you can also  read .trr file by the use of matlab code
>>>>
>>>>>
>>>>> On Wed, Nov 26, 2014 at 9:01 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> On 11/25/14 9:04 PM, 石锐 wrote:
>>>>>>
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have generated a large .trr file (~500 G) from a simulation. To
>>>>>>> save
>>>>>>>
>>>>>>>  the
>>>>>>
>>>>>
>>>>>  space, I just want to write a C/C++ code to read and manipulate the
>>>>>>
>>>>>>>
>>>>>>>  binary
>>>>>>
>>>>>
>>>>>  .trr file directly rather than convert it to a readable .gro or .pdb
>>>>>>
>>>>>>>
>>>>>>>  file.
>>>>>>
>>>>>
>>>>>  However, I cannot find the format of .trr file from the manual. Is
>>>>>> there
>>>>>>
>>>>>>> anyone who knows how to read the .trr file ?
>>>>>>>
>>>>>>>
>>>>>>>  The XDR library can be used to do this:
>>>>>>
>>>>>> http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 629
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>
>>>>>>
>>>>>> ==================================================
>>>>>> --
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>>>>>  --
>>> _______________________________________________________________
>>> Patrick FUCHS
>>> Dynamique des membranes et trafic intracellulaire
>>> Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
>>> Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
>>> Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
>>> E-mail address: patrick.fuchs at univ-paris-diderot.fr
>>> Web Site: http://www.dsimb.inserm.fr/~fuchs
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>>>
> --
> _______________________________________________________________
> Patrick FUCHS
> Dynamique des membranes et trafic intracellulaire
> Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
> Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
> Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
> E-mail address: patrick.fuchs at univ-paris-diderot.fr
> Web Site: http://www.dsimb.inserm.fr/~fuchs
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.