[gmx-users] water molecule cannot be settled

[MD]

Ok, thank you Justin.
Ming

On Nov 29, 2017 6:55 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 11/29/17 6:53 PM, MD wrote:
>
>> Hi Justin,
>> Can you tell me where you spotted the broken topology? And where should I
>> get in to get it fixed?
>>
>
> "System has non-zero total charge: -0.859995"
>
> Can any molecule have a fraction of an electron?
>
> Whatever you've manually parametrized is incorrect.
>
> -Justin
>
> 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
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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> Gromacs Users mailing list
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