[gmx-users] water molecule cannot be settled

[MD]

Hi Justin,
Can you tell me where you spotted the broken topology? And where should I
get in to get it fixed?
Thanks,
Ming

On Nov 29, 2017 6:15 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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