[gmx-users] read trr file
石锐
rshi at itp.ac.cn
Thu Dec 4 04:17:18 CET 2014
Hi Tsjerk,
I still didn't receive your code. Since the list doesn't allow attachment, would you please send your code to my email (rshi at itp.ac.cn) directly ?
Thanks,
Rui
> -----原始邮件-----
> 发件人: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> 发送时间: 2014年12月2日 星期二
> 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> 抄送:
> 主题: Re: [gmx-users] read trr file
>
> Sorry, that should've been sent off-list. The list doesn't allow
> attachments. I'll try again :)
>
> Cheers,
>
> Tsjerk
>
> On Tue, Dec 2, 2014 at 10:28 AM, 石锐 <rshi at itp.ac.cn> wrote:
>
> >
> > Hi Tsjerk,
> >
> > I cannot find your code in the attachment. Would you please send it to me
> > again off list.
> >
> > Thanks,
> > Rui
> >
> >
> > > -----原始邮件-----
> > > 发件人: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> > > 发送时间: 2014年12月2日 星期二
> > > 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > > 抄送:
> > > 主题: Re: [gmx-users] read trr file
> > >
> > > 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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> > > > > >>>>
> > > > > >> --
> > > > > >> _______________________________________________________________
> > > > > >> 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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> > > >
> > > > --
> > > >
> > > > ====================================================
> > > > 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)
> > > > ====================================================
> > > >
> > > > --
> > > > Gromacs Users mailing list
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> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> >
> >
> > --
> >
> > ====================================================
> > 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)
> > ====================================================
> >
> > --
> > Gromacs Users mailing list
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
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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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