Thank you Jason for your help,
Even though the coordinate array is x (and it is used like this in some
parts of the code),
I cannot seem to find any reference to this array in the non-bonded energy
calculation part of the code in
short_ene.f (This is where i am interested in using them...)
In particular, in the calculation of 6-12 interactions ew_directp.h and
ew_directe.h,
the coordinates seem to be assigned in the arrays:
imagcrds(1,n).... and
xktran(1,itran).
Can you tell me (or anyone else in the mailing list) how are the coordinates
handled in these arrays?
Thanks again,
Antonios
On Wed, May 19, 2010 at 6:42 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> >From my understanding of the code, sander uses a global array structure,
> in
> which all (major?) arrays are simply sections of a much much larger array.
> Thus, there is a real array, integer array, etc, and the positions will
> have
> a chunk of the real array (as will, for instance, the velocities and
> forces,
> etc.). (There are also hollerith arrays and I believe a couple others).
>
> See the file $AMBERHOME/src/sander/locmem.f. The positions, it would
> appear, occupy a section of the real array "x" beginning at position lcrd
> ("LCRD"). This variable is located in the common block, and is the
> variable
> used, I believe, globally to reference the starting position of the
> coordinate array (it may not necessarily be lcrd if lcrd is passed from one
> subroutine/function to another where it is renamed). I also believe the
> array is structured as (x1,y1,z1,x2,y2,z2,...), though someone may correct
> me here.
>
> Hope this helps,
> Jason
>
> On Wed, May 19, 2010 at 6:59 PM, Antonios Samiotakis
> <asamiotakis.gmail.com>wrote:
>
> > Hi,
> >
> > I am trying to find the coordinate arrays used in the source code of
> sander
> > in amber10.
> > In older versions of amber there used to be: X(1,I) X(2,I) and X(3,I)
> > arrays
> > that stored the coordinates.
> > Is there something analogous to this in amber10?
> >
> > Thank you,
> >
> > Antonios
> >
> > --
> > Antonios Samiotakis
> > Department of Physics
> > University of Houston
> > 4800 Calhoun Rd
> > SR1 Rm 629G, Houston
> > TX, 77204
> > e-mail: asamiotakis2_at_uh.edu
> > http://www.phys.uh.edu/~mscheung/antonios.htm<http://www.phys.uh.edu/%7Emscheung/antonios.htm>
> <http://www.phys.uh.edu/%7Emscheung/antonios.htm>
> > <http://www.phys.uh.edu/%7Emscheung/antonios.htm>
> > Tel: 713-743-3725
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Antonios Samiotakis
Department of Physics
University of Houston
4800 Calhoun Rd
SR1 Rm 629G, Houston
TX, 77204
e-mail: asamiotakis2_at_uh.edu
http://www.phys.uh.edu/~mscheung/Antonios.CV/Resume10.2.website.htm
Tel: 713-743-3725
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Received on Tue May 25 2010 - 13:30:06 PDT
