[gmx-users] gmx sasa output confusion
teemu.murtola at gmail.com
Thu Nov 5 17:33:46 CET 2015
The issue with incorrect legends and X axis has been fixed in 5.0.6.
As for the four columns, you are asking gmx sasa to calculate the same
numbers twice, so you get them twice: according to gmx sasa -h, the area of
-surface selection is always calculated, and -output (which is optional)
just specifies extra groups on top of this to calculate the area for.
As for the legends for the extra columns, no one has just had the time to
implement nice output for all possible cases.
On Wed, Nov 4, 2015 at 7:20 PM Francesco Carbone <fra.carbone8 at gmail.com>
> Good afternoon,
> I calculated the residue area (-or) over my trajectory, but I have trouble
> understanding the output.
> With gromacs 4.6 I obtain a clean file:
> residue value standard dev
> 27 4.65478 1.19505
> 28 0.990566 0.966795
> 29 1.77202 0.629798
> 30 0.389708 0.374724
> 31 0 0
> 32 0 0
> 33 0 0
> 34 0 0
> with gromacs 5 instead I see odd things:
> 1) the titles between -or and -oa results are swapped.
> -or gives "title "Area per atom over the trajectory"", while -oa "title
> "Area per residue over the trajectory"".
> xaxis is set correct (res with -or and atom with -oa)
> 2) I have 18 times the same residues plus 4 columns with only s0 and s1
> with legend ("Average" and "Standard dev")
> I'm using this command:
> gmx sasa -s file.tpr -f file.xtc -n file.ndx -or ciao5.xvg -surface Protein
> -output Protein -dt 5000
> Is there some changes I have missed ?
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