AMBER Archive (2006)

Subject: Re: AMBER: RDF output

From: Thomas Cheatham (
Date: Wed Aug 30 2006 - 17:18:29 CDT

> I have tried to calculate the radial distribution functions for specific
> residues with water and I have some questions related with the output:
> 1) The amber 8 manual says that three files are produced, but I didnīt obtain
> the file corresponding to the carnal style RDF. Does anyone know why?

In some versions of ptraj, support for dumping the carnal style RDF was
commented out. You can change this by minor code changes in the actions.c
routine transformRadial().

> 2) The rdf values that come in the second column of the volume.xmgr file are
> all zero but the standard.xmgr file contains the "normal/expected" values. Is
> this correct? What the difference in the values that should I obtain?

The numbers are not zero, just smaller than the precision. In fact, it
looks like this is a bug when doing this type of RDF namely that the
volume is scaled down by the number of frames inappropriately (so the RDF
becomes really small). Ah ha, I see it now, specifically that this will
-only- happen with non-orthorhombic boxes and it is a bug. For now,
either rely on the "standard" or make code modifications to change the
volume, in actions.c, transformRadial(), as below...

   * update total volume
  if (box[3] == 90.0 && box[4] == 90.0 && box[5] == 90.0)
    info->volume += state->box[0] * state->box[1] * state->box[2];
  else {
    xx = cos(box[3]*DEGRAD);
    yy = cos(box[4]*DEGRAD);
    zz = cos(box[5]*DEGRAD);
    info->volume += box[2]*box[1]*box[0]* sqrt(1.0 - xx*xx - yy*yy - zz*zz + 2.0*xx*yy*zz);

That seems to work for me...


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