[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?
dommert at icp.uni-stuttgart.de
Fri Oct 22 16:41:43 CEST 2010
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On 10/22/2010 04:35 PM, Carsten Kutzner wrote:
> On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote:
>> 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
> 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.
as I already mentioned try g_current, which decomposes the total dipole
moment in two parts (rotational and translational).
>> 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
>> 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
>> <mailto:gmx-users at gromacs.org>
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Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
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