VMD-L Mailing List

From: cong chen (vmd_chcwaaa_at_yahoo.com.cn)
Date: Thu May 08 2008 - 20:53:08 CDT

Dear all,
      I tried to read the source code. To calculate a dihedral angle, the subroutine calculate_dihed has been used. And a subroutine normal_atom_coord has been applied to get coordinates. In this subroutine, there are several codes that I am quite puzzled by,
  ////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  // Apply periodic image transformation before returning
    Matrix4 mat;
    now->get_transform_from_cell(cell, mat);
    mat.multpoint3d(pos, pos);
  ///////////////////////////////////////////////////////////////////////////////////////////////////////////////
  The author said that it is to apply periodic image transformation before returning, but I traced the code step by step and found that the array "pos" has not been changed anymore by using mat.multpoint3d.
    I am quite puzzled. VMD processes NAMD outputs which contain the true positions of the atoms. Why are the coordinates not changed here ? For calculating RDF, the coordinates have been changed if periodic boundary condions have been applied.
    I would be most appreciative if some could give me any advice.

       
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