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 calculation? Regards -- Ozge Engin ★☆
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