[gmx-users] water molecule cannot be settled

[Justin Lemkul]

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

==================================================