[gmx-users] can gromacs read amber trajectory
David van der Spoel
spoel at xray.bmc.uu.se
Sat Feb 18 21:25:28 CET 2006
Lydia wrote:
> I'm checking. For box, is it 3*10 or 3*8 per frame? I do see
> difference in the defined format between .g87 and amber for the box as
> the following:
In fact the gromacs software does just read floats, and with the fixed
format it is possible that numbers are printed without spaces. This will
break the gromacs input routine. Your best bet is maybe to either hack
the gromacs source (src/gmxlib/trxio.c routine do_read_xyz) or to
preprocess your trajectories with a (Perl) script which enforce a space
between the numbers.
In principle you can read fixed format with C as well, but I'v enever
tried to see if that works reliably.
> For .g87:
>
> --------------------------------------------------------------------------
> TITLE
> x(i) (10f8.3)
> box(m) (10f8.8)
> ----------------------------------------------------------------------------
>
>
> For amber:
> ---------------------------------------------------------------------------------------
>
>
> AMBER trajectory (coordinate or velocity) file specification
>
> This file is optionally written during dynamics in SANDER or GIBBS.
>
> FORMAT(20A4) ITITL
> ITITL : the title of the current run, from the AMBER
> parameter/topology file
>
> The following snapshot is written every NTWX steps in the trajectory
> (specified in the control input file):
>
> FORMAT(10F8.3) (X(i), Y(i), Z(i), i=1,NATOM)
> X,Y,Z : coordinates or velocities (velocity units: Angstroms per 1/20.455 ps)
>
>
> IF constant pressure (in 4.1, also constant volume)
>
> For each snapshot:
>
> FORMAT(10F8.3) BOX(1), BOX(2), BOX(3)
> ---------------------------------------------------------------------------------------
>
>
>
> sincerely
> lydia
>
> On 2/18/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> Lydia wrote:
> > I don't want to rerun because there are too many to rerun. But I
> > still want to use gromacs analysis tool which is very powerful.
>
> Then you'll have to debug a bit further. I suspect the file and the
> software go out of sync somewhere. Does it work to read 100 frames? 10
> frames? 1 frame? (Use the -e option again).
>
> You should be able to read 1 frame and compute hbonds on it.
>
> Also you could try to check the file size. If you have Natom atoms then
> the file size should be Natom*3*8 bytes + 3*10 bytes (box) per frame,
> plus 80 bytes for a title. Thus
> Filesize = 80 + Nframe * ( Natom*3*8 + 3*10 )
> It might be that an extra character is stored per line in the file
> (newline), this you could take into account by subtracting the number of
> lines in the file (wc file.g87)
>
> Good luck...
>
> > Lydia
> >
> > On 2/18/06, *Lydia* < aether2006 at gmail.com
> <mailto:aether2006 at gmail.com> <mailto:aether2006 at gmail.com
> <mailto:aether2006 at gmail.com>>>
> > wrote:
> >
> > Amber mdcrd trajectory has the same format of .g87 (title,
> x(i)
> > and box).
> > I tried g_hbond -e 750 but it gave me the same. I notice
> that in
> > the manual, you have .g96 instead .g87 mostly. Is it because .g87
> > can not be read and analyzed any more? Thank you for your
> help and
> > information.
> >
> > sincerely
> > Lydia
> >
> > On 2/18/06, *David van der Spoel* < spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>
> > <mailto: spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>>
> wrote:
> >
> > Lydia wrote:
> >> If I calculate hbond it won't give error information but the
> >
> > try g_hbond -e 750
> > to see whether the beginning of the traj is OK.
> >
> > If the format is not as expected I don't know how to fix it.
> > Maybe you
> > can mould our trajecotry into another format using some
> kind of
> > script.
> > Otherwise just try and rerun the simulation...
> >
> >> hbnum.xvg will be
> >>
> >
> -----------------------------------------------------------------------------------------------------------------
> >
> >> cat hbnum.xvg
> >>
> >> # This file was created Sat Feb 18 08:44:34 2006
> >> # by the following command:
> >> # g_hbond -f nmwt.g87 -s nmwt.tpr -n index.ndx -num -hbm -a 120
> >> #
> >> # g_hbond is part of G R O M A C S:
> >> #
> >> # GRowing Old MAkes el Chrono Sweat
> >> #
> >> @ title "Hydrogen Bonds"
> >> @ xaxis label "Time"
> >> @ yaxis label "Number"
> >> @TYPE xy
> >> @ view 0.15, 0.15, 0.75, 0.85
> >> @ legend on
> >> @ legend box on
> >> @ legend loctype view
> >> @ legend 0.78, 0.8
> >> @ legend length 2
> >> @ s0 legend "Hydrogen bonds"
> >> @ s1 legend "Pairs within 0.35 nm"
> >> 801 11 4
> >>
> >
> ----------------------------------------------------------------------------------------------------------------
> >> I'm expecting 800 rows of numbers which are the number of
> > hbonds
> >> as a function of time (800ps). But it has only one row to
> > give out
> >> the average number of hbonds per timeframe 11.000 out of 330
> > possible.
> >>
> >> Best wishes
> >> Lydia
> >>
> >>
> >>
> >
> ------------------------------------------------------------------------
> >>
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> >
> >
> > --
> > David.
> >
> ________________________________________________________________________
> >
> > David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
> > spoel at gromacs.org <mailto:spoel at gromacs.org>
> <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
> > http://xray.bmc.uu.se/~spoel
> <http://xray.bmc.uu.se/%7Espoel <http://xray.bmc.uu.se/%7Espoel>>
> >
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> >
> ------------------------------------------------------------------------
>
> >
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>
> --
> David.
> ________________________________________________________________________
>
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://xray.bmc.uu.se/~spoel
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>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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