[gmx-users] Solvent is added inconsistently

Dawid das addiw7 at googlemail.com
Mon Sep 9 22:25:27 CEST 2019

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
I get a slightly different number of solvent (water) molecules. This makes
obviously, because after deleting the crystallographic water molecules,
is slightly more space to be filled.

However I noticed that presence of some water molecules added by solvate
buried inside the protein cavities depends on whether these three initial
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
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

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

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