On Tue, 6 Jan 2009 18:46:39 +0800
Dechang Li <[email protected]> wrote:
Dechang Li wrote:
Dear all,
I want to use g_rotacf to calculate the order parameter(S2, N-H bond in
main chian).
The tool g_rotacf needs an index.ndx file that contains two vectors.
g_rotacf wants the index number of two atoms to calculate the order
parameter of an NH vector. You should give the index number of the atoms
N and H and use the option -d. Note that you have to take care of the
overall rotation of the molecule in the calculation. Either you remove
it before the calculation or you include it in the fit of the correlation
function.
I read the manual that the index file should contain 3 atoms, i.e. (i, j,
k).
Is that mean I should write the index file like this:
[ group1 ]
1 3 4
[ group2 ]
5 8 9
where 1 for atom Ca, 3 for atom N, and 4 for atom H, in a peptide?
This will not define a vector! To follow the movement of the NH vector
(made of two atoms! the N and the H) you need only two index numbers, the
one of the N and the one of the H. Then the option -d is needed for
g_rotacf to treat the corresponding vector.
Thank you for your reply! It was helpful. It was said that the index
file only need 2 atoms, i.e. index of N and H. However, for the residue
PRO, how to define the vector NH?
There is typically no signal for the residue Pro.
How can I make the
index.ndx file? Can I use the tool make_ndx to do this? Or I need to write
the file manually?
See http://wiki.gromacs.org/index.php/Index_File. I think you just want
to write a file by hand.
Mark
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-----------------------------------------------------
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------
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-----------------------------------------------------
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------
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