Hi, I have two questions about using g-helix and g_rotacf On g_helix, 1. I have used the following command: "g_helix -s md.tpr -f md.xtc -n index.ndx -b 10000 -e 20000" In the index file, I have residues 10-20 as my group. However, when I ran the above command, I did not have the n-ahx.xvg file. Did I miss something here? On g_rotacf, I have used the following commands to calculate the order parameters: "trjconv -s md.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans" to remove the rotational and translational motion of my protein. " g_rotacf -s md.tpr -f fit.xtc -d -n nh - P 2 ". In the index file, it lists all the NH pairs except the N atoms from proline. It gave order.xvg and rotacf.xvg. In terms of getting the correct order parameters for each NH, are the above 2 commands correct? Finally, in the manual, it mentions about the triplet, i, j, k. What is the meaning of the triplet?
Thanks for your insights! Simon
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