[gmx-users] Strange grompp error: System has non-zero total charge
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Jan 8 02:29:07 CET 2009
Suman Chakrabarty wrote:
> Hi,
>
> I am trying energy minimization with a simple alkane chain in a DMSO
> box. So there should not be any unbalanced charge on any individual
> molecule. Each atom of the alkane is uncharged and DMSO has following
> entries in dmso.itp file:
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 SDMSO 1 DMSO SDmso 1 0.139 32.06000
> 2 CDMSO 1 DMSO CDms1 1 0.16 15.03500
> 3 ODMSO 1 DMSO ODmso 1 -0.459 15.99940
> 4 CDMSO 1 DMSO CDms2 1 0.16 15.03500
>
> So total charge on a DMSO is zero.
>
> But when I run grompp for the energy minimization it complains:
>
> NOTE 1 [file topol.top, line 548]:
> System has non-zero total charge: -4.882812e-04
A difference from zero this small can be ignored, since it results from
arithmetic problems with using approximate floating-point
representations of exact decimal values. For example, 0.02 cannot be
represented exactly, and it is well known that (something like) adding
0.02 to itself one hundred times does not give a floating-point result
that is numerically equal to two.
Mark
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