[gmx-users] Energy Minimization

[Steven Neumann]

Dear Gmx Users,

I am setting up my simulations of carbon tube with protein. I solvated my
system, added ions and I would like to run EM of my system. My carbons of
the tube in MD will be restrained. In this case should I run EM of my
protein in water (and with ions) separately and the copy coordinates and
then process with NVT and NPT or run EM with restrained nanotubes of my
system directly?

Thank you,

Steven
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