[gmx-users] g_rdf

xiaoyi li xiaoyi at xray.bmc.uu.se
Thu Nov 6 12:33:01 CET 2003


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 ]
[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?

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

What's the problem? What should I do?

Best Regards,

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