[gmx-users] Problem sasa 3.2.1 vs 3.3.2

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 18 21:59:29 CEST 2008

Hi Anthony,

It's not even that different. The order is swapped (the colors) and
the most notable difference is that the noise is higher in the newer
version. The running averages will probably give very similar results.
Still interesting to know what happened to the noise. The answer is
probably in the source (and may be in a head belonging to a



On Thu, Sep 18, 2008 at 3:39 PM, Anthony Cruz <acb15885 at uprm.edu> wrote:
> Hi users:
> Recently I run a simulation of a protein in DMSO with GROMACS 3.2.1. I make
> the analysis with GROMACS 3.3.2 and GROMACS 3.2.1 .  When I do the sasa
> analysis I observe differences in the sasa values between the two versions.
> The total sasa seems to be same in the two graphs but the hydrophobic and
> hydrophilic looks very different (see attached pictures).
> What could be the problem? Which version will be the best for analysis?
> Cheers,
> Anthony
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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