[gmx-users] Re: Your Question about unwanted waters

[Anton Feenstra]

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 <ababakha at mccammon.ucsd.edu> 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

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