[gmx-users] read trr file

[Tsjerk Wassenaar]

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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