Hey guys,
the following command uses the -surf flag and it causes some unnormalized-looking g(r) (see attached png file):
gmx_mpi rdf -s tpr.tpr -ref 'resname TST' -sel 'resname RER -f movie.xtc -o test.xvg -bin 0.03 -surf res
Any idea why? And how do I fix this?
Hello,
the -surf flag in Gromacs produces an unnormalized radial distribution function.
Quoting from the Gromacs manual:
"For -surf, the selection provided to -ref must select atoms, i.e., centers of mass are not supported. Further, -nonorm is implied, as the bins have irregular shapes and the volume of a bin is not easily computable."
With -nonorm, only the number of groups in -ref is used for normalization, leading to the output you observed. If you need a normalized rdf, you should remove the -surf flag.
Hope this helps.
Andrea Arsiccio Thanks for your reply. So what is the purpose of the -surf flag?
How is the unnormalized rdf useful?
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