[gmx-users] Best method for equilibrating lipid system (Amber parameters)

[Crystal Vander Zanden]

Dear Gromacs Community,

I am trying to determine the most appropriate way to equilibrate my system
which contains lipid, protein, and water.

I built the system using CHARMM-GUI, but I used only the .pdb coordinates
and instead I parameterized it with Amber using the Lipid17, ff14SB, and
tip3p water force field parameters.  Now I'm doing my simulations in
Gromacs.

My guess is that since I'm using Amber force fields, I should use
equilibration parameters comparable to something like this tutorial for
equilibrating and running in Amber with Lipid14 force field?
http://ambermd.org/tutorials/advanced/tutorial16/#Minimization
However Charmm-gui recommended a 6-step equilibration process which
gradually removes restraints on the lipids and then the protein. (assuming
use of Charmm36 force field).
The Gromacs lipid tutorial uses a fairly straightforward equilibration
process.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/05_EM.html

And once equilibrated, what is the best way to run production?  I see a lot
of discussion about the importance of using proper non-bonded cutoff
schemes.

Thanks in advance for any advice!  I want to make sure I'm doing this
correctly.
Crystal

-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque