On 6/17/12 7:56 AM, delara aghaie wrote:
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
There is no absolute way to say anything about which is better. You should be
choosing your analysis based on what you want to measure or observe. An SDF for
a protein and an SDF for solvent will be wildly different quantities.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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