When calculated during the md run, the corresponding options in g_energy
for the dipole moment are MU-X, MU-Y and MU-Z.
However, taking into account the previous mail by David van der Spoel,
it's possible that the dipole moment could not be calculated in your
system. Options in g_energy vary depending on the actual computation.
If you want to calculate the dipole moment by your own, I think it's
easier to use the xtc file exported every 3fs (it'll be considerably
heavier than the edr file, however) and writing an specific code for
your purposes. In order to read the trajectories, you can use the xtc
library
(http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library).
Anyway, if the code didn't compute it, there should be a reason.
Javier
El 19/10/12 04:42, Nilesh Dhumal escribió:
Is it possible to calcualte the dipole moment at 3fs by modifing the
source code?
Nilesh
How can I save the total dipole moment extacted by .edr file?
I could not find the option in g_energy.
Nilesh
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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