[gmx-users] Using g_densmap

Mark Abraham mark.abraham at anu.edu.au
Tue May 18 20:54:48 CEST 2010

Please use a descriptive subject line to help everybody.

I suspect your use editconf is your problem. -princ may not preserve your box the way you've assumed. Try -princ -c, or editconf -princ then editconf -c.

It's also pointless and error-prone to compile MPI versions of the GROMACS tools. Only mdrun is MPI-aware, and the installation guides make this clear.


----- Original Message -----
From: Ricardo Cuya Guizado <rcuyag at hotmail.com>
Date: Wednesday, May 19, 2010 4:14
Subject: [gmx-users] RE: gmx-users Digest, Vol 73, Issue 109
To: gmx-users at gromacs.org

  <!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 10pt; font-family:Verdana } --> -----------------------------------------------------------

> Dear Friends
  I tried to obtain the XY density maps of the heme using g_densmap tool.
  The molecule was centered in the box
  The system was rotated to maintain the XY plane on the molecular plane.
  In the reference gro file, the molecule was also centered and the plane XY was on the molecular plane.
  To create the reference gro file
  editconf_mpi_d -f heme.gro -c -o heme_centered.gro -n index.ndx -princ
  To center the molecule in the box
  trjconv_mpi_d -f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s dmpr.tpr -center -boxcenter rect -pbc atom
  Rotations and translations were eliminated and the XY axis on the XY molecular plane
  trjconv_mpi_d -f md10ns_heme_centered.xtc -o md10ns_heme_centrado_centered_rottrans.xtc -n index.ndx -s heme_centered.gro -fit rot+trans
  To obtain the XY density map
  g_densmap_d -f md10ns_heme_centrado_centered_rottrans.xtc -s heme_centered.gro -n index.ndx -o densmap.xpm 
  The result show the molecule in the corner of the figure and a diffuse withe region around the molecule.


> I will expect a more defined region around the molecule and centered.
  I need help, thanks
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