[gmx-users] g_rdf

[David van der Spoel]

On Thu, 2003-11-06 at 13:30, xiaoyi li wrote:
> Hello,
> 
> I am sorry to disturb you with such basic questions, but I couldn't find
> them out from Manual and Mailing list.
> 
> I would like to calculate the rdf between a hydroxylic hydrogen (type A)
> and oxygens on water (type B). In the index.ndx file, i should define:
> [ type A ]
> 1
> [type B ]
> 4 7 10 ...
> 
> My questions are:
> 
> 1. Should I write out all of the numbers (in corresponding .gro file) of
> oxygens on water under type B? If so, how could I do for such a lot of
> atom numbers?
use make_ndx
> 
> 2 When I try to calculate and run: g_rdf -f -s *.tpr -n -o
> It shows: Fatal error: No such option -grid in pargs
> If I run: g_rdf -f -s *.tpr -n -grid 0.05 -o
> It shows: Unknown argument: -grid
> Unknown argument: 0.05
> Fatal error: Program gmx-ana halted

remove the grid option

> 
> What's the problem? What should I do?
> 
> Best Regards,
> Xiaoyi
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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