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

Teemu Murtola teemu.murtola at gmail.com
Sun May 29 21:17:23 CEST 2016


On Fri, May 27, 2016 at 9:19 PM Eric Smoll <ericsmoll at gmail.com> wrote:

> (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'
> indicate?

You are correct about 'res': it refers to a residue, which is typically
inferred from residue numbers and names. 'mol' stands for molecule, and can
be used with .tpr input, where it refers to molecules specified in the

> (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?

Yes, this is correct. Also if the selections are identical, you can still
use the -sf flag twice, with the same file both times. It is also possible
to put both selections into the same file and just use -sf once, after both
options (like -ref -sel -sf file.dat).

Best regards,

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