[gmx-users] Water molecule cannot be settled

[Steven Neumann]

On Fri, May 18, 2012 at 12:38 PM, Javier Cerezo <jcb1 at um.es> wrote:

>  Hi Steven
>
> You've tried with "constraints = none", but that still keeps constraints
> over water molecules through SETTLE algorithm. Maybe you can try a
> minimization with "define = -DFLEXIBLE" to remove settle over water and
> then try again a constraint (settle) minimization.
>
> Javier
>

Awesome! Thank you Javier, that really helped!!!!

Steven


>
> El 18/05/12 12:58, Steven Neumann escribió:
>
> 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
> forces)
> coulombtype    = PME        ; Treatment of long range electrostatic
> interactions
> 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
> error
>
> 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,
>
> Steven
>
>
>
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
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