[gmx-users] g_sas command with the -q option

Ozge Engin ozge.engin at gmail.com
Thu Apr 15 13:14:27 CEST 2010

Hi all,

I have a system which is composed of hexane-peptide-water-peptide-hexane
layers. There, I selected the hexane+peptide system as the calculation
group, and the hexane group as the output group to calculate the hexane area
that is in contact with water. To do this I used the g_sas command with the
-q option. I looked at the connelly.pdb file via vmd. I think the
calculation and the output groups are shown in that file. I saw that the the
upper, right and left sides of the simulation box have been included which
means to me the periodic boundaries are not taken into account during the
calculation. In addition, when I use the g_sas command I get a warning as
the following:

WARNING: Analysis based on vacuum simulations (with the possibility of
evaporation)will certainly crash the analysis. Turning off pbc.

So, the periodic boundary is taken into account or not during the sas

Ozge Engin
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