VMD-L Mailing List

From: Andrew DeYoung (adeyoung_at_andrew.cmu.edu)
Date: Sat May 26 2012 - 16:14:52 CDT

Hi,

Thanks. Yes, it seems that VMD thinks my system has zero dipole moment. I
am just not sure how to correct this.

Andrew DeYoung
Carnegie Mellon University

________________________________

From: Wang Yi [mailto:dexterwy_at_gmail.com]
Sent: Saturday, May 26, 2012 3:27 PM
To: Andrew DeYoung
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Another thought related to drawing dipole moment vectors

VMD will show a 3-D arrow representing the dipole of your selected atoms. I
guess the reason you didn't see it, is that VMD thinks your system has zero
dipole --> no arrow.

___________________________

Yi (Yves) Wang
Duke University

On 2012-5-26, at $B2<8a(B1:27, Andrew DeYoung wrote:

        Hi again,
        
        If the Gromacs configuration and trajectory file formats indeed do
not
        support the inclusion of charge information, and if this will make
        monitoring the dipole moment using Dipole Moment Watcher, then I can
think
        of one potential workaround.
        
        I can use the Gromacs utility g_dipoles to calculate the x, y, and z
        components of the dipole moment as a function of time (in addition
to the
        norm of the dipole moment vector as a function of time) and print
this
        information to a text file.
        
        So a possible workaround would be to somehow animate a 3-D arrow in
VMD so
        that I can watch how the dipole moment vector changes as I watch the
        trajectory. Is it possible to input a list of vector components and
draw
        the corresponding vector on the respective frames of the trajectory?
        
        Thank you!
        
        Andrew DeYoung
        Carnegie Mellon University