On 2011-05-25 20.42, Nilesh Dhumal wrote:
Basically I want to calculate the stretching vibration of the bond by
fourier transfrom of dipole momenet autocorrelation fucntion or velocity
autocorrelation function.
Before going for vibration I wanted to check the fluctuation of dipole
moment along the simulation.
Can I calculate the velocity autocorrelation function for a bond.
Of course.
How about g_velacc
Nilesh
On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote:
On 2011-05-25 18.03, Nilesh Dhumal wrote:
Thanks for reply.
Here are more details about my simulation.
I have glucose molecule in my system. I am interested in change in
dipole moment of OH bond of glucose along the simulation.
The OH group is not neutral so your dipole is meaningless (position
dependent).
Otherwise the charges are constant and the fluctuation in bond length
(if you have a flexible molecule) will be small, or zero with
constraints. You should think what you want to get out. What experiment you
want to compare to.
I have made the index file.
How can I select two groups (oxygen and hydrogen) or should I put
particular oxygen and hydrogen in same group (manually).
Nilesh
On Wed, May 25, 2011 11:59 am, David van der Spoel wrote:
On 2011-05-25 17.36, Nilesh Dhumal wrote:
I want to see the change in dipole moment alond the simulation.
g_dipoles -h
NIlesh
On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:
On 2011-05-25 17.14, Nilesh Dhumal wrote:
Hello,
Can I calculate a dipole moment of a particular bond?
It is easier to do it manually. Otherwise g_dipoles with a
suitable index file would do it. The sum of charges has to be zero
of course.
I am using gromacs version 4.0.7.
Thanks
Nilesh
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Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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