[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!
jnsong
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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