[gmx-users] SDF problem

Daniele Veclani danieleveclani at gmail.com
Tue Sep 22 14:14:05 CEST 2015

Dear gromacs user

My system consist of 1 molecule + 1000 of solvents (water) in cubic
box.  I did 5 ns NPT equilibration and currently I am doing analysis stuff
such as RDF, density, viscosity, etc. And now I want to try using g_spatial
I stuck on it. I would like to know if you can help me in this.

In Gromacs manual, they wrote like this:

1. Use make_ndx to create a group containing the atoms around which you
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface

I have tried to follow those steps but I coud not get any pretty SDF

This is what I have done following the above mentioned steps:
step 1: I have my index file
step 2: I choose my molecule ("solute") as group for centering
and I select "system" (1 molecule + 1000 solvents) as an output group
step 3: Again, I choose "solute" and choose "system" as an output
step 4: I run g_spatial and select "1000 solvents" for both calculation and
output. It gives me warning to increase nab values, so I increase the nab =
100. I got grid.cube but the size of the file is not that big (the manual
it is around 3 copies of *.xtc file).
step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of
solvents there on the VMD display

How can I view the molecule?

I use Gromacs 5.0.4.


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