[gmx-users] g_spatial index file

[Mark Abraham]

On 16/02/2012 3:03 PM, Paymon Pirzadeh wrote:
> Hi,
> I used g_select to choose the hydration shell molecules of my protein
> from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to
> feed the generated index file into g_spatial to calculate the SDF of
> solvent around my protein. However, when I feed this into the g_spatial,
> it lists 1500 group and my protein. How can I tell the command to use
> the 1500 groups to calculate the SDF?

You will need to use something like a shell script to loop over each 
group and match it with its frame. See 
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts 
for clues.

> Or can I specify a dynamic selection when I run the g_spatial? sth like
> "resname SOL and within 1.0 of protein"?

Not yet. This kind of functionality will exist in GROMACS 5.0

Mark