GROMACS version: 2019
GROMACS modification: No
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I want to calculate distance between centroids of Tyr and Trp. Can I use center of geometry for this? I don’t know how exactly GROMACS describes COG and if it would be appropriate for residues like TRP.
Thanks for your reply. I have read the syntax and able to get the results but data doesn’t seem right. I have used following command:
gmx_mpi distance -f file.xtc -s file.tpr -n cog.ndx -oav distancecentroid.xvg
cog.ndx:
[A]
854 852 850 849 857 859
[B]
981 979 977 976 984 986
where A is ring 1 and B is ring 2. I made the file manually.
As you explained in this post that the difference between gmx pairdist and gmx mindist that pairdist has min as well as max values while mindist only has min value. Both seems equally appropriate to me as far my problem is concerned. However, mindist is also not giving me intuitive values.
Hi,
I though you were interested in the cog distance. gmx mindist does not have any option to set it, while gmx pairdist has the option to define cog for the ref and select groups.
Best regards
Alessandra