-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 10/22/2010 04:35 PM, Carsten Kutzner wrote: > 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 >>
Hello, as I already mentioned try g_current, which decomposes the total dipole moment in two parts (rotational and translational). /Flo >> >> 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@gromacs.org >> <mailto:gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzBoqcACgkQLpNNBb9GiPmjKgCgtWB3ye0NFAFAWN/JrgY/8Eh2 mqIAn0zW4QOYzDvsEXE+Ygee3itfpYqe =CNXQ -----END PGP SIGNATURE----- -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
