[gmx-users] Re: Genion and number of Ions

David spoel at xray.bmc.uu.se
Thu Sep 26 16:50:17 CEST 2002

On Thu, 2002-09-26 at 16:31, Marc Saric wrote:
> I checked my chains (the *.itp-files), and did not find any error, all 
> residues have integer charges.
> Due to the fact that this is a bit tedious to do for ~ 1000 Residues, I 
> wrote a small python-script (if anyone is interested...) to check (of 
> course it finds wrong chargegroups if I insert some ;-) ).
> The charge-error is reported by grompp, the itp-files look reasonable.
If all molecules have integer charge there is something weird. It is
quite easy to check the topology file manually using binary search.
Start at the bottom, then look half way the topology and so on. 
2 log 1000 = 10.

> Any further idea? Should I simply ignore this and believe, that it is a 
> rounding error? Does something might goe wrong further down the road 
> (water-addition, compilation of EM-Input)?
Well, I would be rather upset to find something like this only after a
few days of calculations, so better look into it now...

> I'm running GROMACS 3.1.4 on a SGI Origin with MIPS R12000 Processor, 
> Chip Revision: 3.5, FPU: MIPS R12010 Floating Point Chip Revision: 0.0
> and Irix 6.5. GROMACS has been compiled with single precision and fftw 
> 2.1.3 from fftw.org.
Shouldn't make any difference.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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