[gmx-users] read trr file

[Patrick Fuchs]

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