Dear Aparamita, trjconv can enable or preclude subsequent analysis of trajectories, depending on what you want to do. For example, by fitting chosen groups to a reference structure. By centering your protein, you effectively remove all lateral diffusion, so it’s not surprising that a very low diffusion coefficient is reported for the processed trajectory.
Kind regards, Erik > On 17 Nov 2016, at 08:53, Apramita Chand <apramita.ch...@gmail.com> wrote: > > Dear All, > I had one doubt regarding g_trjconv which I used to center my protein after > simulation. I got different diffusion values when I used the .xtc file > before and after applying trjconv. Which one should be used? Is trjconv > just for visualisation or is necessary for analysis too? Does it change the > values or interactions in any way? > For example, the diffusion values that I got were > Before trjconv After Trjconv > Urea - 1.6628 2.089 > Protein - 0.0927 0.000108 > Water 2.513 2.59 > > Please advise. Which values should be taken? > > Regards > Apramita > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
