[gmx-users] read trr file

Patrick Fuchs patrick.fuchs at univ-paris-diderot.fr
Tue Dec 2 10:48:51 CET 2014 

Hi Tsjerk,
thanks for that, but I can't find anything attached.
Best,

Patrick

Le 02/12/2014 09:25, Tsjerk Wassenaar a écrit :
> 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
>> --
>> Gromacs Users mailing list
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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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