[gmx-users] spatial distribution function

delara aghaie d_aghaie at yahoo.com
Sun Jun 17 13:56:38 CEST 2012

Dear Gromacs users.
I have simulated a single chain protein in water for 5 ns. Now I want to calculate spatial distribution function. To do this I use command g_spatial. I have read manual for that. I need to have an index group containing the atoms around which the SDF is wanted.

It is not clear to me, which atoms to use for such an analysis. 

It is better to calculate SDF of solvent or protein? which one is more informative?
any suggestions would be greatly appreciated

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