[gmx-users] gmx sasa

[Justin Lemkul]

On 1/31/16 2:24 PM, Eric Smoll wrote:
> Hello Gromacs Users,
>
> "gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii
> are obtained from the following reference:
>
> "A. Bondi, van der Waals Volumes and Radii, J.
> Phys. Chem. 68 (1964) pp. 441-451"
>
> Can the user still control the radii used by editing a local copy of the
> share/gromacs/topvdwradii.dat file?
>

Of course (and you can test this in a few seconds by making a change and seeing 
if it affects your results).

The message is only there to indicate a significant change that has been made 
since previous versions, one that will affect the results of the analysis such 
that they will not reproduce those of old versions (because the source of radii 
is now better).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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