[gmx-users] Could g_order be used to calculate the order parameters for the two bonds C1'-H1', C3'-H3' in DNA?

jnsong jnsong at itcs.ecnu.edu.cn
Mon Nov 14 12:09:46 CET 2011

Dear all,

Recently, I have performed simulation on a B-DNA using gromacs, and I
want to use g_order in gromacs to get the order parameters for the bonds
C1'-H1', C3'-H3'. Is it possible to obtain order parameters for these
two bonds with g_order? If possible, Would you please tell me the
correct way to get order parameters for C1'-H1', C3'-H3'?

Thank you very much!


P.S. I just had a try using g_order, the process is as follows:


> a C1'

Found 24 atoms with name C1'

 11 C1'                 :    24 atoms

> a H1' 

Found 24 atoms with name H1'

 12 H1'                 :    24 atoms

> del 0-10

Removed group 0 'System'
Removed group 1 'DNA'
Removed group 2 'K'
Removed group 3 'CL'
Removed group 4 'Water'
Removed group 5 'SOL'
Removed group 6 'non-Water'
Removed group 7 'Ion'
Removed group 8 'K'
Removed group 9 'CL'
Removed group 10 'Water_and_ions'

> q

through this I get index.ndx for C1'-H1' and 

then I perform: 

> g_order -f md.xtc -s md.tpr -n index.ndx -o

and I get order.xvg, but there are no order parameters in order.xvg and 

the contents of order.xvg are as follows:

# This file was created Thu Nov 10 20:00:06 2011
# by the following command:
# g_order -f md.xtc -n index.ndx -s md.tpr -o -ob 
# g_order is part of G R O M A C S:
# GROup of MAchos and Cynical Suckers
@    title "Order tensor diagonal elements"
@    xaxis  label "Atom"
@    yaxis  label "S"
@TYPE xy

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