[gmx-users] Non-zero total charge and Floating Point Arithmetic

[Justin Lemkul]

On 2/14/17 3:37 AM, Мижээ Батсайхан wrote:
> Dear gmx users,
>
> I got following note. Please advice me? I checked all topologies in my
> system, but I could not find floating point.
>
> NOTE 1 [file topol.top, line 36]:
>   System has non-zero total charge: -14.999997
>   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.
>

This is the textbook example of what that page describes.  The total charge is 
the sum of a large number of floating-point values.  So there is a small 
rounding error.  Your system clearly has a net charge of -15.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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