GROMACS version: 2023.2
GROMACS modification: Yes/No
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Hello everyone,
I am a new GROMACS user. I have the system with a surface at the bottom of the box, and add water (Ow and Hw), and Zn atoms above the surface (total z length = 10 nm). Here, I would like to calculate the RDF/CN between Zn and Ow in the z < 4.5 nm range region. I have tried to use gmx select to generate new ndx:
gmx select -f XXX.xtc -s XXX.tpr -select ‘name ZN OW and z<4.5’ -on ZN_OW_Lower45A.ndx
Then,
gmx rdf -f XXX.xtc -s XXX.tpr -o RDF.xvg -cn CN.xvg -n ZN_OW_Lower45A -b 4000 -e 8000
The program shows:
Available static index groups:
Group 0 “name_ZN_OW_and_z<4.5_f0_t0.000” (2431 atoms)
Group 1 “name_ZN_OW_and_z<4.5_f1_t1.000” (2432 atoms)
Group 2 “name_ZN_OW_and_z<4.5_f2_t2.000” (2476 atoms)
.
.
.
Group 3613 “name_ZN_OW_and_z<4.5_f3613_t3613.000” (2505 atoms)
Group 3614 “name_ZN_OW_and_z<4.5_f3614_t3614.000” (2493 atoms)
Group 3615 “name_ZN_OW_and_z<4.5_f3615_t3615.000” (2269 atoms)
Specify a selection for option ‘ref’
Could you suggest how to use gmx select, or is there a way to do this?
Thank you,
Athis
