[gmx-users] water molecule cannot be settled

[Justin Lemkul]

On 11/29/17 3:26 PM, MD wrote:
> Hi,
>
> I was trying to minimize a solvated structure with following commands but I
> got stuck at an error message complaining about water molecule not settled
> when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
> mdrun command, log file and the error message after the command. Any help
> will be appreciated.
>
> 'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'
>
> NOTE 1 [file em_real.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
>
> Setting the LD random seed to 2057414563
> Generated 97877 of the 97903 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 64492 of the 97903 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
> Excluding 3 bonded neighbours molecule type 'Other_chain_B'
> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
>
> NOTE 2 [file topol.top, line 53]:
>    System has non-zero total charge: -0.859995
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>

You have a fundamentally broken topology. Don't attempt any simulation 
with such a topology until you correct it.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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