[gmx-users] make_hole vs. genconf

[Arneh Babakhani]

Dear GMX Users,


I'd like to build some lipids around a peptide.  Can I do so using 
genconf?  (I know genconf can be used to build a membrane.  I'm asking 
if genconf can be used to build a membrane around a solute, like a 
transmembrane protein?)


I'm also aware of the make_hole tool.  My question here is:  Does 
make_hole create a hole of specified dimensions and orientation, 
according to the solute coordinates?  And can you specify exactly where 
in the membrane you want the whole?


So basically what I'm asking is:  If you want to make a starting 
structure (or several structures) with the solute (a peptide) in a 
specific part of the membrane, is it better to set the desired 
coordinates of the peptide first and then build a membrane around it?  
Or, is it wiser to start with an equilibrated membrane and use make_hole 
to create your hole first at the desired coordinates, then insert the 
peptide?


Thanks,

Arneh