-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 10/16/2010 10:28 PM, David van der Spoel wrote: > On 2010-10-16 21.36, Chih-Ying Lin wrote: >> >> Hi >> I issue the g_dipole command on Gromacs => And, the following >> information is shown. >> There are 10 molecules in the selection, >> Does the Average =32.1611 refer to the average for a single over the >> simulation time? >> Or, the Average = 32.1611 summing for all the 10 molecules over the >> simulation time? >> If the average = 32.1611 for a single molecule with 33 atoms / united >> atoms of most carbon groups, isn't the dipole moment too high? > I think this is the average per molecule. You may need to run trjconv > -pbc whole, because mdrun may break molecules in two parts, meaning that > the molecule becomes as big as the box. > > >> >> >> >> >> What does "will subtract their charge at their center of mass" this >> mean? >> Why "will subtract their charge at their center of mass" ? >>
It is not a trivial task do determine the dielectric constant of a system containing charged molecules. Many articles have been published about this subject. The net-charge of a the molecule is subtracted at the center of mass to decompose the dipole moment into a rotational and translational part. I do not in what property of your system you are exactly interested, but there is also the tool g_current which can determine the rotational and translational part of the dipole moment. /Flo >> >> >> >> ================================================================== >> There are 10 molecules in the selection >> There are 10 charged molecules in the selection, >> will subtract their charge at their center of mass >> Using Volume from topology: 220.317 nm^3 >> >> Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1# >> >> Back Off! I just backed up aver.xvg to ./#aver.xvg.1# >> Last frame 10000 time 20000.000 >> Average volume over run is 221.043 >> >> Dipole moment (Debye) >> --------------------- >> Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095 >> > > - -- 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/ iEYEARECAAYFAky6+qIACgkQLpNNBb9GiPmjbwCgpse3SksYDm0smAdxMlQOtiQG 0k0An3bX2WG3auOTyQLwciESYoGefCCO =eR6W -----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