Thank you for the guidance, David. Now I got it, but a thing that also helped was to set the option -pbc inbox in trjconv, which I didn't know if I had to (I read the manual, but even so, I didn't know). Now I see the water dipole counterbalances the entire protein one (I was testing in PolyALA, so no effect of the residues. Now I'll test in my helix)
Thank you again, Gustavo > [EMAIL PROTECTED] wrote: > > 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 > > > > > I would do both the helix backbone, and the entire helix, so that you > can test whether the sidechains compensate for the net dipole or the > other way around. You could also look at the net dipole of the water > with resect to the helix. > > As for trjconv, please read the manual about aligning structures > (trjconv -h) > > 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
