[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

[Carsten Kutzner]

On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote:

> 
> Hi
> Sorry, I ask the same question again because i am not a decent person in this field.
> If possible, someone can give me a quick answer while i am trying to get understanding the source codes.
> My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the following equation.
> dipole moment = 48.0 sum of q_i x_i
> x_i is the atomic position.
Gromacs does not have another approach. It exactly calculates the above
equation. Take a look at the function "mol_dip( )" in gmx_dipoles.c. There,
the dipole moment is calculated for a single molecule. A molecule is a group 
of atoms connected by chemical bonds. g_dipoles will only consider the
molecules of the group you are prompted to provide. If you for example
choose 'solvent' then you will get the sum of all the individual dipole
moments of the water molecules in your system. 

Carsten
> 
> 
> When I issued the command g_dipole,
> the dialog poped out and asked me to select a group.
> 
> 1. system
> 2. protein
> ....
> .....
> ....
> 11. solvent
> 12. the rest of the salt-molecule except its counter ion
> 13. counter ions (CL-)
> 
> 
> If I select #12, Gromacs will not consider counter ions to calculate the
> dipole moment ???
> 
> 
> Sorry for disturbing people in the Gromacs mailing list.
> Thank you
> Lin
> 
> 
> On 2010-10-22 00.49, Chih-Ying Lin wrote:
> > Hi
> > When I issued the command g_dipole,
> > the dialog poped out and asked me to select a group.
> > 1. system
> > 2. protein
> > ....
> > .....
> > ....
> > 11. solvent
> > 12. the rest of the salt-molecule except its counter ion
> > 13. counter ions (CL-)
> > If I select #12, Gromacs will not consider counter ions to calculate the
> > dipole moment ???
> > Thank you
> > Lin
> >
> you should try to understand what is going on yourself rather than
> sending many email to the mailing list. Please read the source code of
> the program.
> 
> --
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101022/2605c78a/attachment.html>