Justin Lemkul wrote:
Hello all,
I have a quick question regarding an MD simulation I am attempting to run
(again, the membrane protein which I had problems with previously). Thanks to
the helpful suggestions; my system is now well-minimized! The last step before
I would like to take before running full-out MD on my system is to equilibrate
my solvent and ions over a short timeframe (100ps). My initial attempts have
been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps)
before I get a screen full of LINCS warnings. Apparently one of my DPPC
molecules is being blown apart. I have placed position restraints on both my
protein and my bilayer, in order to allow the solvent and ions (Na+) to move
around them. I have attached my equil.mdp file below, in case I am making any
obvious mistakes. I am piecing my .mdp file together from several examples and
tutorials.
Don't couple temperature for ions and solvent seperately. Make a
combined group and couple that.
Have you tried visualising you equilibration through to the point things
start exploding? That may highlight a problem.
Mark
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