[gmx-users] Building and Equilibrating a United-Atom DOPC-DPPC-Cholesterol Bilayer

John Smith nimzster at yahoo.com
Tue May 3 09:02:02 CEST 2016

Hello all,
I have been attempting to build a proper united-atom DOPC-DPPC-Cholesterol bilayer for use in simulations for a while. At first I used CHARMM-GUI and then backward after equilibration to convert the coarse-grained equilibrated bilayer into a UA representation, but the resulting membrane system was not usable for my simulations because a couple DOPC molecules popped out of the bilayer, cholesterol molecules were in the middle of the bilayer, and so on. This does not seem like physically reasonable behavior. To get around this problem, I decided to keep all the molecule center of masses the same in the XY plane, but reorient them to point along the z-axis and recenter them in z so that all molecules in the top and bottom leaflets, respectively, would have the same center of mass in z. I then ran several rounds of energy minimization on this recentered system. However, when I use the result and attempt to run equilibration I am getting LINCS warnings (relative constraint deviation after LINCS), and then fatal errors of the form "1 particles communicated to PME node 15 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y." From what I understand, the LINCS warnings are usually a sign that the system is not well equilibrated. But how can I correct this without even being able to equilibrate my system? Running the energy minimizations for even longer doesn't seem to fix the issue.
Please help as I am really not sure how to proceed.

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