[gmx-users] Calculating the radius of gyration of clusters

[GAYATHRI S]

Dear all,

I ran MD simulations of a small molecule and clustered structurally
similar frames together. I wanted to find the radius of gyration of all
the members of each cluster.

To do the same, I used the command:

$ g_gyrate -f cluster.xtc -s full.tpr -o cluster_rg.xvg

Here, the file "cluster.xtc" was obtained as output from the g_cluster
command.

When I ran the above command, I got the following error multiple times:

There were 10 inconsistent shifts. Check your topology.

Is there a better way of finding the radius of gyration of all the cluster
members in a given cluster? Please suggest how I should go about.

Thank you

Regards,
Gayathri