[gmx-users] bilayers with genconf

[Peter Tieleman]

I think building bilayers with genconf works quite well. What we have done is align a lipid in a square box along the z-axis, say 1x1 nm to avoid overlap between lipids, use genconf with the random translation and random rotation option (rotate around z, translate along z by rand(0.5 nm)), build a single leaflet of 64 lipids. Rotate (don't mirror) and translate that leaflet to make the other leaflet (editconf). The bilayer will be too large because of the 1x1 nm initial box, but you can scale to the approximately right box size with editconf -scale. Minimizing restores the geometry, add water with genbox, remove water with a script from the hydrocarbon interior, equilibrate. 

Peter
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Dr. D. Peter Tieleman, Associate Professor, AHFMR Scholar
Dept. Biological Sciences, University of Calgary
2500 University Dr. NW Calgary, AB T2N1N4 Canada
Fax: (403) 289-9311 Web: http://moose.bio.ucalgary.ca