[AMBER] Best practices for lipid equilibration - Amber parameters in Gromacs

From: Crystal Vander Zanden <cvanderzanden.unm.edu>
Date: Mon, 22 Jan 2018 09:13:30 -0700

Dear Amber 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 understanding is that lipid equilibration is not trivial, and I want to
be sure I'm doing it correctly. My guess is that I should choose an
equilibration protocol based on the force field I'm using (not the
software)? 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/

In contrast, Charmm-gui recommended a 6-step equilibration process which
gradually removes restraints on the lipids and then the protein (this
assumes use of Charmm36 force field).
Here is an example of a lipid equilibration in Gromacs (parameterized with
Gromos force fields).

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
AMBER mailing list
Received on Mon Jan 22 2018 - 08:30:02 PST
Custom Search