[gmx-users] gmx sasa output confusion

[Francesco Carbone]

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")

   27    1.845    0.314    1.845    0.314

      27    0.962    0.341    0.962    0.341

      27    1.089    0.184    1.089    0.184

      27    0.686    0.145    0.686    0.145

      27    0.086    0.066    0.086    0.066

      27    0.111    0.064    0.111    0.064

      27    0.002    0.007    0.002    0.007

      27    0.002    0.009    0.002    0.009

      27    0.000    0.000    0.000    0.000

      27    0.001    0.004    0.001    0.004

      27    0.002    0.007    0.002    0.007

      27    0.026    0.031    0.026    0.031

      27    0.002    0.014    0.002    0.014

      27    0.339    0.113    0.339    0.113

      27    0.271    0.071    0.271    0.071

      27    0.875    0.151    0.875    0.151

      27    0.901    0.226    0.901    0.226

      27    0.010    0.022    0.010    0.022
      28    0.352    0.131    0.352    0.131
      ...

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 ?

Regards,

Francesco