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!
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
