[gmx-users] SDF problem

Justin Lemkul jalemkul at vt.edu
Wed Sep 23 00:43:14 CEST 2015

On 9/22/15 8:14 AM, Daniele Veclani wrote:
> 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
> but
> 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
> want
> 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
> picture
> 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
> says
> 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?

By saving the solute coordinates (the output group in g_spatial) rather than the 
solvent molecules.  You will also need to adjust the isosurface value in VMD to 
get anything sensible.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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