[gmx-users] sasa calculation with different gromacs versions

[Justin A. Lemkul]

Rocco Caliandro wrote:
> 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?

Several hundred lines of code are different in between gmx_sas.c between version 
4.0.7 and 4.5.3, so I'd suspect something similar in the case of 4.0.2 vs. 
4.5.1.  Most notably, in 4.0.x, no effort is made to account for periodicity.

-Justin

> Cheers,
>                      Rocco
> 
> 
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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