Hello, I am trying to calculate free volume of polymers using two methods. The first one is using a script I modified based on one script found in the forum. The lines for calculate free volume of Connolly surface with r=0 is shown below. Another method I tried is in tools--> Atoms Volumes and Surfaces, and I also set the Connolly surface with r=0. But the two methods gives me quite different results. The script gives me free volume % ~ 12%, while the Atoms Volume and Surfaces tool gives me free volume percentage of >30%. Can anyone help me to unsderstand why the methods give so different results? Thanks.

HY

#####################################Connolly surface with r=0 (van de Waals surface)

my \$field = \$tempDoc->CalculateConnollyField;
my \$isosurface = \$field->CreateIsosurface([IsoValue => 0,
                                            HasFlippedNormals => "YES", IsoSurfaceKind => "normal"]);

my \$freeVolume = \$isosurface->EnclosedVolume;

\$study->Cell(\$rowCounter, 9) = \$freeVolume;

my \$isosurface = \$field->CreateIsosurface([IsoValue => 0,
                                            HasFlippedNormals => "No", IsoSurfaceKind => "normal"]);

my \$OccupiedVolume = \$isosurface->EnclosedVolume;

\$study->Cell(\$rowCounter, 10) = \$OccupiedVolume;
my \$FreeVPercentage=\$freeVolume/(\$freeVolume+\$OccupiedVolume)*100;
\$study->Cell(\$rowCounter, 11) =\$FreeVPercentage ;