[gmx-users] g_helix and g_rotacf

simon sham ssham44 at yahoo.com
Sat May 28 00:24:12 CEST 2011

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 

Thanks for your insights!


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