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 http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas
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