Hi David Thank you very much for the reply! So, which group, in the end, shall I select in g_dipoles to see the dipole? And how to use trjconv after editconf the way you told me? (the input/output of editconf is a .gro file and of trjconv is .trr/.xtc files) And whose group shall I select in the least squares/output prompts in trjconv -fit trans+rot?
Thank you very much, Gustavo > [EMAIL PROTECTED] wrote: > > Hello > > > > I'm a beginner user of GROMACS, and I'm currently trying to simulate some > alpha > > helices in an explicit water box to extract some initial structures for > > subsequent quantum mechanical calculations (which uses pbc as well). I'd > like > > to know if there's a way to check if the dipole moment of the protein > backbone > > is screened by the water, the way it should be, because if not, the results > > from QM will be incorrect for what I want to observe. I checked the results > > with g_dipoles_d and below is what I got, for 500ps 300K NVT MD of a 20 > residue > > polyalanine in a box of 1813 water molecules (total of 5651 atoms, 1nm > from the > > edges of the helix), but I'm not certain where to look to decide if it's > correct > > (of course, a frame won't necessarily have a zero dipole moment, but maybe > it > > seems too high? If you look at the Mtot.xvg, the total dipole is between > 240 > > and 60 Debye). Any help would be appreciated! > > > did you select just the helix backbone for this calculation? probably > not, and then you are looking at the water. in addition you probably > want to align the helix to the box otherwise you are looking at the > average of a moving helix. editconf -princ and then use trjconv -fit > rot+trans to fit the trajectory on the first structure. > > > Thanks in advance, > > Gustavo > > > > > > Dipole moment (Debye) > > --------------------- > > Average = 2.3041 Std. Dev. = 1.2691 Error = 0.0042 > > > > The following averages for the complete trajectory have been calculated: > > > > Total < M_x > = 39.2483 Debye > > Total < M_y > = -54.7993 Debye > > Total < M_z > = 59.1645 Debye > > > > Total < M_x^2 > = 9509.68 Debye^2 > > Total < M_y^2 > = 14277.5 Debye^2 > > Total < M_z^2 > = 17721.9 Debye^2 > > > > Total < |M|^2 > = 41509.1 Debye^2 > > Total < |M| >^2 = 8043.83 Debye^2 > > > > < |M|^2 > - < |M| >^2 = 33465.3 Debye^2 > > > > > > > > ---------------------------------------------------------------- > > This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ---------------------------------------------------------------- This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
