[gmx-users] read trr file

石锐 rshi at itp.ac.cn
Thu Nov 27 03:25:31 CET 2014


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
> >>>>>
> >>>>>
> >>>>> ==================================================
> >>>>> --
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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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