[gmx-users] Regarding difference in SASA values using GMX versions 5.X and 4.X

[Mark Abraham]

Hi,

On Thu, May 28, 2015 at 5:23 PM bipin singh <bipinelmat at gmail.com> wrote:

> Hi all,
>
> I have calculated SASA for a group amino acid residues using GMX versions
> 5.0.1 and 4.6.3 and noted that there is significant difference in the
> calculated values, as can be seen in figure at the link below.
>
>
> https://drive.google.com/file/d/0ByHdYJNF-aRrTEFtNDR5dEEyZlU/view?usp=sharing
>
> I know that it is already mentioned that from version 5.0 GMX uses the Van
> der Waals radii from paper "A. Bondi, van der Waals Volumes and Radii, J.
> Phys. Chem. 68 (1964) pp. 441-451", and it is expected to be different
> compared to previous GMX versions. However I wanted to know what was the
> source of Van der Waals radii in GMX 4.X versions


History is silent, so probably someone made stuff up in a vaguely plausible
manner.

and which one is
> considered to be more accurate.
>

"Accurate" depends on the purpose, and requires someone to show that
certain radii correlate best with whatever other quantities. (How big is an
electron cloud, anyway?) For observing qualitative differences in solvent
accessibility of two configurations, probably any guess is as good as
another...

Mark


>
> ------------------------------
> Thanks and Regards,
> Bipin Singh
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