<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Oct 22, 2010, at 4:14 PM, Chih-Ying Lin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><div>Hi</div><div>Sorry, I ask the same question again because i am not a decent person in this field.</div><div>If possible, someone can give me a quick answer while i am trying to get understanding the source codes.</div>
<div>My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the following equation.</div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">dipole moment = 48.0 sum of q_i x_i<br>
x_i is the atomic position.</span></div></blockquote>Gromacs does not have another approach. It exactly calculates the above</div><div>equation. Take a look at the function "mol_dip( )" in gmx_dipoles.c. There,</div><div>the dipole moment is calculated for a single molecule. A molecule is a group </div><div>of atoms connected by chemical bonds. g_dipoles will only consider the</div><div>molecules of the group you are prompted to provide. If you for example</div><div>choose 'solvent' then you will get the sum of all the individual dipole</div><div>moments of the water molecules in your system. </div><div><br></div><div>Carsten<br><blockquote type="cite"><div><br></div><div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">When I issued the command g_dipole,<br>
the dialog poped out and asked me to select a group.<br><br>1. system<br>2. protein<br>....<br>.....<br>....<br>11. solvent<br>12. the rest of the salt-molecule except its counter ion<br>13. counter ions (CL-)<br><br><br>
If I select #12, Gromacs will not consider counter ions to calculate the<br>dipole moment ???</span></div><div><br></div><div><br></div><div>Sorry for disturbing people in the Gromacs mailing list.</div><div>Thank you</div>
<div>Lin</div><div><br></div><div><br></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">On 2010-10-22 00.49, Chih-Ying Lin wrote:<br>> Hi<br>
> When I issued the command g_dipole,<br>> the dialog poped out and asked me to select a group.<br>> 1. system<br>> 2. protein<br>> ....<br>> .....<br>> ....<br>> 11. solvent<br>> 12. the rest of the salt-molecule except its counter ion<br>
> 13. counter ions (CL-)<br>> If I select #12, Gromacs will not consider counter ions to calculate the<br>> dipole moment ???<br>> Thank you<br>> Lin<br>><br>you should try to understand what is going on yourself rather than<br>
sending many email to the mailing list. Please read the source code of<br>the program.<br><br>--</span></div>
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