[gmx-users] long-stick molecule solvation

xy21hb xy21hb at 163.com
Tue Nov 3 15:58:13 CET 2015

Dear all,

I have a long-stick "carbon-nanotube" like protein to solvate with its length of ~ 220 A and diameter of 50 A.
I tried using a triclinic box with the longest box axis aligned to the C-alpha of the protein, and the protein seems to be properly solvated.
However, energy minimization with GROMACS 5.0 shows,
"There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 9.59877 nm"
Any suggestions on that?



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