I want to create a representation in vmd to view only the hydrophobic (non polar) region of lipid bilayer. How can we do that ? Also, can we measure the length of that hydrophobic region using vmd.
There are many ways how you can do this. All depends on you identifying which atoms belong to the headgroup region and which belong to the hydrophobic region.
Probably the easiest way if you are not interested in the hydrogens of the hydrophobic region is to know the name of carbon atoms in the head group region. e.g. for POPC, you can make the selection:
(lipid and carbon) and not name C1 C2 C3 C1 C11 C13 C15.
Thank you sir. Since my lipid bilayer is a POPC system, the selection that you gave to me worked perfectly. But, since I actually want to remove the water from the hydrophobic region, I want to measure the length of the hydrophobic region or just identify the Z-axis values for which the hydrophobic region lies. Is there anything we can do for it ?
your hydrophobic region will be between z0 and z1 (see below):
set sel [atomselect top "(lipid and carbon) and not name C1 C2 C3 C11 C13 C15"]
set xx [measure minmax $sel]
set xx0 [lindex $xx 0]
set xx1 [lindex $xx 1]
set z0 [lindex $xx0 2]
set z1 [lindex $xx1 2]
I recommend something like:
protein and not hydrogen within 2 of (name C CA CB CG CD CE)
In my case is to hide nonpolar hydrogen on VMD, using GROMACS output file from OPLS-AA force field.
Kind regards.
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