[gmx-users] Solvent is added inconsistently

[Dawid das]

Dear All,

I am facing an issue I do not fully understand. Namely, let's take two
crystallographic structures of the same protein and in one of them let's
delete three crystallographic water molecules that are not buried inside
the protein (let's forget about a reason for it for a moment).

Now, when I use exactly the same procedure to generate the box and the
solvent
I get a slightly different number of solvent (water) molecules. This makes
sense
obviously, because after deleting the crystallographic water molecules,
there
is slightly more space to be filled.

However I noticed that presence of some water molecules added by solvate
and
buried inside the protein cavities depends on whether these three initial
water
molecules were deleted or not.

Why is that? I know that after deleting the water molecules the centering
of my protein (with its remaining crystallographics water molecules) is
somehow
different but why does it affect the position and/or presence of some newly
added water molecules?

Best wishes,
Dawid Grabarek

PS I use gromacs 2016.3
PPS I use following commands:
gmx pdb2gmx -f $name.pdb -o "$name".gro -p "$name".top -water tip3p -his
-glu

gmx editconf -f "$name".gro -o "$name"-box.gro -bt triclinic -d 1.2 -princ

gmx solvate -cp "$name"-box.gro -cs spc216.gro -p "$name".top -o
"$name"-solv.gro