[gmx-users] 'gmx rdf' and 'gmx select' questions

Eric Smoll ericsmoll at gmail.com
Fri May 27 20:18:52 CEST 2016

Hello Gromacs users,

I have a few syntax questions:

(1) What is the difference between 'res' and 'mol' position specifiers? I
assume 'res' refers the set of all atoms that have the same gro-file
residue-number *and* residue name. Is this correct? What does 'mol'

(2) 'gmx rdf' in Gromacs 5.1.2 allows the user to specify the '-ref' and
'-sel' groups with 'gmx select' style selection strings on the commandline.
It appears that there is an option to provide selections from a file with
the '-sf' flag. 'gmx help selections cmdline' suggests that  '-sf file.dat'
should be provided as an argument to a selection. If the '-ref' and '-sel'
groups are not identical, can this flag be used twice with two different
files? For example:

gmx rdf -ref -sf file1.dat -sel -sf file2.dat

Is this correct?


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