[gmx-users] Water molecule cannot be settled

Steven Neumann s.neumann08 at gmail.com
Fri May 18 12:58:47 CEST 2012

Dear Gmx Users,

My system consists of a Tube made of Oxygen, Hydrogen and ions. These atoms
are not connected via bonds. I try tu run EM:

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save

integrator    = steep    ; Algorithm (steep = steepest descent minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep        = 0.001
nsteps        = 50000    ; Maximum number of (minimization) steps to perform
nstxout     = 1
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist    = 1        ; Frequency to update the neighbor list and long
range forces
ns_type    = grid        ; Method to determine neighbor list (simple, grid)
rlist        = 1.4        ; Cut-off for making neighbor list (short range
coulombtype    = PME        ; Treatment of long range electrostatic
rcoulomb    = 1.4        ; Short-range electrostatic cut-off
rvdw        = 1.4        ; Short-range Van der Waals cut-off
pbc        = xyz         ; Periodic Boundary Conditions (yes/no)

freezegrps = TUB
freezedim  = Y Y Y

Then a lot of errors "water molecule on atom X cannot be settled". I tried:

1. constraints = none

2. remove those water molecules - then other water molecules have the same

3. using nstxout =1 in VMD, I could observe that some of the molecules
facing this error split in one frame (hydrogens 7A away from oxygen) or
spin around 180 degrees - it depends.

4. I tried increase vdwradii of the atoms which form my Tube so they wont
overlap with water

If you have any suggestions I will really appreciate,

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