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
Gromacs.
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/
advanced/tutorial16/#Minimization
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).
*
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
<
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.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
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Received on Mon Jan 22 2018 - 08:30:02 PST
