[gmx-users] about total charge

[Erik Marklund]

You wouldn't happen to use the AMBER-port and nucleic acids, would  
you? In that case you should look out for an issue with the  
aminoacids.dat that can cause non integer total charge.

/Erik

23 apr 2007 kl. 11.27 skrev Tsjerk Wassenaar:

> Hi Riu Li,
>
> Now, add 0.28 Na+ ion to your system.
>
> Check your topology, it doesn't add up somewhere. The sum of the
> partial charges should be integer (taken into account a rounding
> error).
>
> Cheers,
>
> Tsjerk
>
> On 4/23/07, Rui Li <moonfine at mail.sdu.edu.cn> wrote:
>> Dear all,
>>
>> When I use grompp,it warns:
>> NOTE:
>>   System has non-zero total charge: 1.172000e+01
>>
>> So I add 12 Cl- in my system.
>> Then I use grompp again,it warns:
>> NOTE:
>>   System has non-zero total charge: -2.799983e-01
>>
>> How can I make the total charge zero?
>>
>>
>>
>>
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>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys