[gmx-users] sasa calculation with different gromacs versions

[Rocco Caliandro]

Hi everybody,

   I found a discrepancy in the sasa calculation
between gromacs versions 4.0.2 and 4.5.1.
For a trajectory generated by gmx 4.0.2. with AMBER force fiels,
 I calculated the sasa values  by using the g_sas module taken
from gromacs 4.0.2 (a) and gromacs 4.5.1 (b).
I  list the results for three representative residues:
          (a)     (b)
res 1  0.58  0.35
res 2  1.10  1.05
res 3  0.27  0.05

I got a rough agreement by changing the probe radius
from 0.14 to 0.10  in g_sas from gromacs 5.4.1 (b'):
         (a)     (b')
res 1  0.58  0.66
res 2  1.10  1.00
res 3  0.27  0.34

Could you explain me the reason for such discrepancy?
Cheers,
                     Rocco




-- 
                       Dr Rocco Caliandro
                   Istituto di Cristallografia
               Consiglio Nazionale delle Ricerche
             via Amendola 122/o, 70126 Bari - Italy
                       Tel ++39 080 5929150
                       Fax ++39 080 5929170
                    rocco.caliandro at ic.cnr.it
                          www.ic.cnr.it