[gmx-users] genion in gromacs 3.3.1

[David van der Spoel]

Miguel Ortiz Lombardia wrote:
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> Dear colleagues,
> 
> It looks like genion behaviour has changed in gromacs 3.3.1 as compared
> to 3.3
> 
> I still have both binaries in my machine and when using identical inputs
> to add some Na cations the new one (3.3.1) adds them randomly, while the
> previous one adds them at the most favorable electrostatic potential
> positions, as I intended to. I have looked in the (v. 3.3) documentation
> but I have failed to find a reason for this. Should I change something
> in my input file (or at the command line) in order to get genion from
> v.3.3.1 adding the cations non-randomly?
> 
You can try -norandom. I was under the impression that the potential 
based placement was broken (had been for a while).


> Thank you for your help, and sorry if it was a trivial question.
> 
> Cheers,
> 
> 
> Miguel
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> email: molatwork at yahoo.es
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>                                                        Georges Brassens
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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