[gmx-users] The "correct" way to equilibrate a membrane / lipid bilayer w/water?

Peter C. Lai pcl at uab.edu
Fri Mar 25 04:09:39 CET 2011


I haven't played with gromacs in years, so I'm pretty new at the ability
to play with large systems like lipid bilayers.

What is the "correct" or lets say canonical method to equilibrate a 
membrane patch of say 9x9 nm POPC with sufficient vertical waters to take
care of pbc and long range interactions (> 1.5nm above/below the bilayer)
using Tom's Charmm36 FF port.

I am seeing a lot of different methods out there to: construct and
equilibrate such a system in prepration for g_embed or whatever.

I see from 
the ability to use genbox to replicate Tieleman's 128 patch 

but I also can build my bilayer inside VMD, which supports charmm36->pdb
atom names (and things seem to work fine)

I have yet to see anybody's run parameters and constraints for running
the equilibration, particularly using charmm36 (using vdwtype=switch).
Should I constrain all heavy atoms in the lipid during the NVT run, or
just the polar group (or even just P) and allow the tails to "melt" as seen 
elsewhere? Should I only set Z axis constraints? How long should I run in 
NVT before switching to NPT and for how long (10ns?) And should I change the
constraints moving from NVT to NPT?
How should the thermostat be coupled? System or separate the water from the 

I experienced the same thing as Ng Hui Wen back in October with waters
being extremely dehomogenized (and diffusing out of the box) after 100ps 
NVT with all heavy POPC constrained at 1000 kJ/nm for all axes. I am sure
that moving to NPT will restore the waters but still it was a bit scary to 
see for the first run.

If a lot of these approaches haven't been published, maybe we can just
stick them in the wiki to let everyone "pick their poison" when it comes
to equilibrating their bilayers.

Thanks for any ideas/hints/suggestions

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |

More information about the gromacs.org_gmx-users mailing list