g spatial

The g_spatial program calculates the spatial distribution function (SDF) and outputs it in a form that can be read by VMD as Gaussian98 cube format.  To properly calculate a meaningful SDF, the solute of interest must be centered within the unit cell over the course of the trajectory, and rotational and translational motion must be removed.  That is, the SDF for some surrounding species must be assembled based on a relatively fixed reference.  Several iterations of trjconv are necessary to satisfy these requirements.  Special index groups for your analyzed groups may be required, and would then be passed to trjconv with the -n flag.  These requirements are provided in the manual description for g_spatial, but some additional information regarding the underlying theory is appropriate here.  To carry out a correct g_spatial calculation, follow these steps:

1. Remove periodicity, center the solute

trjconv -s topol.tpr -f traj.xtc -o noPBC.xtc -pbc mol -ur compact -center

Choose the solute as the group to be centered, and any meaningful subset of atoms as the output group.  The entire system is the safest option, otherwise you only really need your solute and the molecule(s) of interest for SDF calculation.

2. Remove rotational and translational motion from the solute

trjconv -s topol.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans

Again, choose the solute as the group from which rotation and translation are removed, and some relevant subset of atoms (or the entire system) as the output group.

3. Run g_spatial on fit.xtc (choosing the molecule(s) around your solute for which you want an SDF for both the calculation and output groups) and load the isosurface in VMD or some other visualization software that is compatible with Gaussian98 cube format.