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bilayer thickness
- gourav
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12 years 8 months ago #764
by gourav
bilayer thickness was created by gourav
i am doing tutorial of simulating lipid bilayer thickness,i am having doubt in calculating bilayer thickness in tutorial its given that we have to take distance between the headgroup peaks in the density profile to get bilayer thickness, which peaks we have to select there lot peaks in density profile.
thanking you
thanking you
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- djurre
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12 years 8 months ago #765
by djurre
Replied by djurre on topic bilayer thickness
Dear Gourav,
If there are many peaks, probably something went wrong. Somethings you should check are:
-If you look at the simulations (eg using ngmx or vmd) has a stable bilayer formed and is it perpendicular to the Z-axis and not moving in the Z direction).
-When creating the density profile (using g_density) are you selecting 1 index group, is this the correct one (eg does it only contain the headgroups, check by looking at the index file or using make_ndx). The number of atoms in index group should be equal to the number of lipids.
If there are many peaks, probably something went wrong. Somethings you should check are:
-If you look at the simulations (eg using ngmx or vmd) has a stable bilayer formed and is it perpendicular to the Z-axis and not moving in the Z direction).
-When creating the density profile (using g_density) are you selecting 1 index group, is this the correct one (eg does it only contain the headgroups, check by looking at the index file or using make_ndx). The number of atoms in index group should be equal to the number of lipids.
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