Justin is right. I've slipped a bit, that was not the way to set
nstenergy. But still, you can save the dipole directly in the edr file.
Not from your existing trajectory, but in a new run. Say your dt=1fs,
then you should set nstenergy=3 to get your dipole moment every 3fs
which you can retrieve with g_energy.
Javier
El 18/10/12 20:43, Nilesh Dhumal escribió:
In short, I can not save dipole moment directly. I can calculate dipole
moment only using .trr file.
Nilesh
On 10/18/12 1:45 PM, Javier Cerezo wrote:
Hi
The dipole is stored in the edr file, which output frequency is
controlled by
"nstenergy" option in the mdp parameter file. Set it appropriately
during your
run (nstenergy=0.003) but keep in mind that it should be a multiple of
the time
step.
nstenergy cannot be set this way; it is an integer indicating the interval
(in
number of steps) for writing energy values. If the values have been saved
every
2 ps, there is no way to retrieve them every 3 fs; if more frequent
information
is needed, it needs to be saved more frequently.
-Justin
El 18/10/12 18:09, Nilesh Dhumal escribió:
Hello,
I am calculating the dipole moment auto-correlation function for my
system
which have 128 cation and 128 anion.
I am saving the trajectory at each 2 ps and using this trajectory for
further analysis.
Can I save the dipole moment and three vectors at each 3 fs?
Thanks
Nilesh
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Physical Chemistry
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