Gromacs Distance

User discussions
1

GROMACS version: 5.1.5
GROMACS modification: No
Respected community members, I am a beginner in Gromacs. I have one quick question. I ran a 50 ns simulation of protein in water. I want to calculate the distance between two carbon atoms of adjacent amino acids during the course of simulation (50 ns).
First I have made the index by using the command
gmx make_ndx -f em.gro -o index.ndx

a 659 (Carbon atom of interest)
Enter (creates a new group 15)
a 3305 (Carbon atom of interest)
Enter (creates a new group 16)
15 | 16
Enter (merge the two and creates a new group 17)
q
Now I used the command
gmx distance -s md.tpr -f md_center.xtc -n index.ndx -oav -oall
Then when prompted I selected group 17 and control+D to end. Then I got average distance with standard deviation and a output distance.xvg graph. Now, when I repeated the same gmx distance command and only used -oall flag I got the same result. Also, when same command was used with just -oav flag I got same result. Now my question is does -oav and -oall give same kind of output answer? Thanks in advance

Thanks in advance

2

I would be highly grateful to any experienced member who can please clarify my doubt in the above mentioned question. Thanks.

3

When computing only the distance between two atoms, -oall and -oav will, by definition, be the same, because there is only one distance that is being considered.