[gmx-users] dppc+mixture

[Dinesh Pinisetty]

Hello all,
          I have taken a mixture of water and methanol,methanol being very
less only around 10% of water molecules(2711 water molecules and 300
methanol molecules).
          I have placed this box with mixture on either side of DPPC 48/48
bilayer.When I performed Energy minimization,all the methanol molecules in
the bottom box escapes into the box which is above i.e on the other side of
the bilayer.Why is this happening is it due to periodic boundary
conditions? but when I checked the minimization(i.e when I have loaded .gro
file in VMD and viewed m.trr file it looks that some methanol molecules are
present in the bottom box) but again when I view the .gro file created
after minimization I cannot see any methanol molecules,can this happen? but
why methanol molecules are moving from bottom box to the above box.
Thanking you,
Yours sincerely,
Dinesh.