[gmx-users] can gromacs read amber trajectory
Lydia
aether2006 at gmail.com
Sat Feb 18 20:56:06 CET 2006
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:
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> 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>>
> > 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>> 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>
> > spoel at gromacs.org <mailto:spoel at gromacs.org>
> > http://xray.bmc.uu.se/~spoel <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 spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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