[gmx-users] read trr file

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 2 09:26:23 CET 2014


Hi Rui,

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 Thu, Nov 27, 2014 at 3:10 AM, 石锐 <rshi at itp.ac.cn> wrote:

>
> If pure Python/numpy can parse TRR file, that would be great. I also want
> to use as less external library as possible.
>
> Best,
> Rui
>
>
> > -----原始邮件-----
> > 发件人: "Patrick Fuchs" <patrick.fuchs at univ-paris-diderot.fr>
> > 发送时间: 2014年11月27日 星期四
> > 收件人: gromacs.org_gmx-users at maillist.sys.kth.se
> > 抄送:
> > 主题: Re: [gmx-users] read trr file
> >
> > 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
> > >>>>>
> > >>>>>
> > >>>>> ==================================================
> > >>>>> --
> > >>>>> Gromacs Users mailing list
> > >>>>>
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> > >>>>>
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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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>
> --
>
> ====================================================
> Rui Shi, Ph.D.
> Visiting Research Fellow
> Institute of Theoretical Physics
> Kavli Institute for Theoretical Physics China
> Chinese Academy of Sciences
> 55 East Zhongguancun Road, Beijing 100190, China
> Email: rshi at itp.ac.cn
> Tel: +86 159-0101-5707 (Cell)
>      +86 10-62648753 (Office)
> ====================================================
>
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-- 
Tsjerk A. Wassenaar, Ph.D.


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