[gmx-users] solvation question regarding waters where they shouldn't be

[David Mobley]

Dear all,

I'm solvating a protein in gromacs using genbox after running pdb2gmx on the
structure. The protein has a small cavity (about the size of several  water
molecules) as well as several other tiny spaces elsewhere, and GROMACS keeps
putting waters in these sites when it solvates the protein. This is
undesirable, as it is actually unfavorable for the water to be in these
spots (they're apolar), but it takes a very long time for the water to make
it out of the protein (>1ns).

Can anyone suggest a good way to prevent water from getting put in these
places in the first place, aside from manually deleting the waters every
time I solvate the protein? I have thought about trying to identify them and
temporarily fill them with LJ spheres  or something, then remove the spheres
after solvating, but that would obviously take some work, and I thought
maybe this would be an issue someone else has already resolved.

Thanks,
David
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