[gmx-users] Re: gmx-users Dipole
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?
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
> 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.
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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