I would like to output per-residue or per-atom sasa information every frame (or every 10th frame, etc). Am I correct that there is no such argument? To be clear I don’t want the average over all frames, I want one value for atom #43 at frame 6, for example.
Is it possible to submit a feature request for this? I know I can clamp the gmx sasa command to a single frame, and then run that command once per frame, but that can take days (estimating 3 seconds to launch and run gmx sasa process for every tenth frame of a 500 ns run = ~2 days.). It seems like it must be much more efficient to do it all in memory in a single multi-threaded process. Is there another faster method that I am overlooking?
Hi,
As far as I understood you would like to calculate the SASA vs time for one or more residues within a protein.
create an index file with a group for the protein and a group for each residue
then run gmx sasa with option -n and -output
select the group of the residues of interest , then Ctrl-D
select the protein group
You will get an area.xvg file with 1+n columns where n are the residues and the first column is the protein area.
To check you can run the average using gmx analyze you should get the average area for each selected residues.
I was not able to find an ‘output all groups’ flag and thus my only options seemed to be interactively typing “1”, “2”, “3”, … “200” or including all the residue numbers on the command line e.g. "-output 1 2 3 4 5 … 200’. This last bit wasn’t so bad, but is this expected or did I miss a step that would automatically include all groups from the index file?
thank you again! I very much appreciate your help.
-denny-