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

bipin singh bipinelmat at gmail.com
Thu May 28 17:22:52 CEST 2015

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.


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 and which one is
considered to be more accurate.

Thanks and Regards,
Bipin Singh

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