A third alternative would be to increase the vdw radii, by copying
vdwradii.dat to your working directory and increase the water radius.
Actually I find that increasing the radius of water can cause the
overall water to be less dense even far away from the protein/micelle.
I do suggest copying vdwradii.dat to your working directory but then
add lines to ensure that the default water radius does not get too
large, e.g. for spc:
??? OW 0.105
??? HW1 0.04
??? HW2 0.04
And then use the -vdwd flag with a value larger than 0.105. This way
your water appears normally to the new waters but the micelle atoms
all seem larger.
Keep repeating with -vdwd values that are slowly getting larger until
you find the minimal value of -vdwd for which no waters are placed
inside the micelle.
Also, how long did you simulate? The water should actually get
squeezed out within 5 ns, and for the size of micelle that has been
simulated in the past you should be able to get 0.5ns-1ns/day.
Chris.
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