Is the total dipole moment stored in the energy file of Gromacs 3.3 correct?
Thanks.
Hao
-----Original Message-----
From: David van der Spoel
Sent: Sunday, November 27, 2011 9:36 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: gmx-users Dipole
On 11/27/11 3:26 PM, Dr. Vitaly V. Chaban wrote:
Dear All,
Is there a way to let GROMACS to calculate and write the total dipole
moment on-the-fly?
I realize that g_dipoles can be used to calculate the total dipole moment
using a stored trajectory. However, for a large system it is not very
feasible to write the trajectory at a frequency good enough for spectra
analysis.
Thanks.
I don't think such way exists, unless you insert the dipole
calculation subroutine into the main code. All gromacs analysis tools
imply postprocessing of the generated trajectories. In certain cases
(e.g. when velocities or forces should be analyzed), this is not
perfect, of course.
This is stored in the energy file still, but THE NUMBERS ARE INCORRECT
since gromacs 4.0.
See http://redmine.gromacs.org/issues/620
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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