[gmx-users] Re: gmx-users Dipole

HAO JIANG jianghao at umich.edu
Mon Nov 28 04:11:07 CET 2011

Is the total dipole moment stored in the energy file of Gromacs 3.3 correct?



-----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 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
spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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