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

Crystal Vander Zanden cvanderzanden at unm.edu
Fri Jan 19 22:58:38 CET 2018

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

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?
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

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

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

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

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