[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Justin Lemkul jalemkul at vt.edu
Mon Jan 15 22:46:15 CET 2018

On 1/15/18 3:52 PM, ZHANG Cheng wrote:
> Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"?

-output is the group you select for output, -o is the file to which the 
data are written. Please read gmx help sasa if you're not clear what the 
options are doing.

> echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns

The command requires two selections, one for the surface, the other for 
what is output. See 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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