[gmx-users] About Area per lipid using Gid-MAT

Poncho Arvayo Zatarain poncho_8629 at hotmail.com
Thu Nov 17 17:09:15 CET 2016

Hello: I'm calculating the area per lipid of a mixed bilayer of dppc and dppe with a molecule inside, using GRID MAT. When i run Grid Mat it appears: Can't calculate the are per lipid, line 761 can't divided by zero in GRID-MAT-MD.pl. So, i check de Grid-MAT.pl in line 761 and this is in: Which is the line that indicates can't divided by zero or which i have to modificate?

# Print APLs just based on number of lipids and cross-sectional surface area
    print "\nCalculating area per lipid head group...\n";

    my $area = $transfer_x*$transfer_y*100;
    my $area_per_lipid_top = $area/(scalar(@top_leaflet_ref));
    my $area_per_lipid_bottom = $area/(scalar(@bottom_leaflet_ref));

    printf ("The lateral area of the system is %.5f sq. Angstroms (per side)\n", $area);
    print "When you don't account for any protein atoms:\n";
    printf ("    The average area per lipid in the top leaflet is %.5f sq. Angstroms\n", $area_per_lipid_top);
    printf ("    The average area per lipid in the bottom leaflet is %.5f sq. Angstroms\n", $area_per_lipid_bottom);

    if ($param{protein} eq("yes")){
        print "When you do take the protein atoms into account:\n";

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