[gmx-users] coordinates file format

[Mark Abraham]

On Wed, Jan 28, 2015 at 11:53 AM, mah maz <mahmaz71 at gmail.com> wrote:

> Dear Mark, Erik
>
> Mark, thank you very much! I asked google and it didn't know either! ;-)
>

Sure it does. https://www.google.com/search?q=libxdrfile. You'd have to
work out how to call its C functions from FORTRAN, though.

your code also didn't work in FORTRAN.


Of course... I did call it pseudocode...

I've searched and found out it is
> not probably an easy task to read a .trr file and even .xtc in FORTRAN.
> Have you got any other ideas?
> Erik, It took me more than 5hrs to read it in FORTRAN and I couldn't
> succeed! I'm not familiar with python. thanks anyway.
>

Reading fixed-width fields from an .xvg file like that written by g_traj
-ox is the only I/O thing FORTRAN77 can do reasonably, so if that's the
only skill set you have available, you'll need to learn how to use FORMAT
and friends :-) Meanwhile, your competitors wrote their code in Python 15
times quicker and published another paper ;-)

Mark


> Regards,
> Mah
>
> On Tue, Jan 27, 2015 at 12:31 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
> > Dear Justin and Mark,
> >
> > I think you are both right.
> >
> > I didn't get your last sentence Mark! What is a libxdrfile?
> >
> > Justin, The problem is I have so many atoms in the system. As I said the
> > best format for reading data is to be like this:
> > time     x1 y1 z1     x2 y2 z2   ....... xn yn zn
> > 0          1 2 3           2 3 4               8 5 6
> > 0.1
> > 0.2
> > ...
> > as you know the trajectory format is like this:
> >
> > (t=)0      x1 y1 z1  x2 y2 z2   x3 y3 z3  x4 y4 z4.......
> > x5 y5 z5   ......... x4000 y4000 z4000
> > (t=)0.1   x1 y1 z1  x2 y2 z2..............
> > x5 y5 z5  ....... x4000 y4000 z40000
> > completely difficult and confusing for me and the program both!
> >
> > According to your points, I can come to the conclusion that changing the
> > file format is not possible.
> > I appreciate your help as usual. thanks alot!
> >
> > Cheers,
> > Mah
> >
> >
> >
> >
> >
> >
> >
> > On Mon, Jan 26, 2015 at 8:01 PM, mah maz <mahmaz71 at gmail.com> wrote:
> >
> >> Dear Mark,
> >>
> >> Thanks for your reply. I think it is not! I have 4000 atoms, the first
> >> number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ....,x4000,
> >> y4000, z4000. They are following each other not in a special order. Then
> >> the next time step starts with x1,y1,z1,....,x4000, y4000, z4000. So,
> they
> >> are not in a column as they are supposed to be. Can I do anything to a
> >> result file to be in my preferable format?
> >>
> >> Many Thanks!
> >> Regards,
> >> Mah
> >>
> >> On Mon, Jan 26, 2015 at 12:08 PM, mah maz <mahmaz71 at gmail.com> wrote:
> >>
> >>> Hi Mark,
> >>> I want to have X Y Z of each atom for all time step apart from other
> >>> atoms so that I can use them as data for programing; like this for
> instance:
> >>> t    x1 y1 z1          x2  y2  z2
> >>> 0    2.4 3.5 4.5       5.6 7.9 9.8
> >>> 0.1  5.5 6.7 8.9
> >>> ...
> >>> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom
> >>> and x2 y2 z2 are for the 2nd atom.
> >>> Is it possible to get the file in a desired format?
> >>> thank you!
> >>>
> >>> On Mon, Jan 26, 2015 at 11:54 AM, mah maz <mahmaz71 at gmail.com> wrote:
> >>>
> >>>> Dear all,
> >>>>
> >>>> I have extracted a file of coordinates after a simulation with 1000000
> >>>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a
> file in
> >>>> which the first column is time and all coordinates are following it.
> Is
> >>>> there a way that I can get coordinates of each time step in a more
> >>>> classified way?
> >>>>
> >>>> Thanks!
> >>>>
> >>>
> >>>
> >>
> >
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