David Mobley wrote:
Arneh,
For the record (since I'm sending this to the users list also), the
problem was that I had a protein with some small "pockets" in it that
are empty in the crystal structure. Some of these pockets were just
large enough that a water molecule could fit in when genbox solvates
the structure, even though no water molecule should be there. In
subsequent simulations, these waters would often remain trapped inside
the protein and drift around, exhibiting very long correlation times.
[...]
On 5/8/06, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
I'm having the same issue (solvating a membrane, and it's placing waters
in the core of the lipid bilayer).
Many people I know who solvate bilayers, actually 'paste' slabs of water
on each side of the bilayer, instead of using genbox. This does leave a
considerable space between the water slabs and the headgroups (except
for the outmost headgroup atoms, that is), but that is relatively easily
equilibrated by restraining the bilayer. If the final density is too low
(happens a lot) and (anisotropic) pressure coupling doesn't quite solve
it (which an also happen often), you may try decreasing the z-box length
in small steps (0.01 nm or so, not scaling, simply change the vector),
and do a bit of md (1 ps or so), again with bilayer restrained.
--
Groetjes,
Anton
* NOTE: New Affiliation, Phone & Fax numbers (below) *
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