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>
> Tel: 713-743-3725
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 19 2010 - 17:00:03 PDT
