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
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