data structure for coding

From: "J. Zheng" <jzheng73 ( ( at ) ) u.washington.edu>
Subject: data structure for coding
Date: Thu, 18 Jul 2002 23:09:38 -0700 (PDT)

 hi CCLers:
   I have a general question about data structure of program. Now I am
 involving a biological system which contains protein, water, ion and
 surface by using MD technique. What I want is to code a general FORTRAN
 program which can deal with single or multiple component system.
  For example, if the system contains protein, water, ion and surface,
 it is very straightforward to assign different components with different
 arrays,
 e.g.
   x(n),v(n),a(n) represent protein coordinate,velocity and acceleration.
   wx(3,n),wv(3,n),wa(3,n) represent water coor., velo. and acce.
   ionx(n),ionv(n),iona(n) represent ion coor., velo. and acce.
   ...
   Now, I am wonder that
 1) is that data structure suitable to deal with biological systems?
 2) how other softwares such as CHARMM, AMBER or GROMACS to handle such
 systems.
    I will appreciate your any suggestion. thanks.
  Jie
  -----------------------------------------------
 |  JIE ZHENG                          	      |
 |  Department of Chemical Engineering	      |
 |  University of Washington		      |
 |  Seattle, WA 98105, USA   		      |
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 |  Tel:  (206) 616-6510 (o)		      |
 | Email: jzheng73 ( ( at ) ) u.washington.edu	      |
 | Webpg: students.washington.edu/jzheng73     |
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