Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall dist.xvg -oh disthist.xvg -b 70000 -e 100000 but don't list r130 and r153 as extra groups. Adding -n *.ndx option didn't sole the problem. Any comment please. -- Gromacs Users mailing list
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