Thank you. I examined the trajectory using VMD and noted that ligand had come out of the binding site and is running around. How is this possible? I have used the guidelines in mdtutorials.com to set up the system. However it's worth noting that there was a power failure around the same time (23ns) and I had to restart MD with append command. Could this have had an affect on MD? Do I have to recreate trajectory file after restarting MD, instead of using the default trajectory?
Regards On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/19 11:59 AM, Quin K wrote: > > Thank you. > > > > I got following when I analysed Ligand RMSD protein backbone as east > square > > fit. > > Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7> > > Can you please comment why there's high fluctuation after like 23 ns? > > What could this mean? > > Watch the trajectory and see what is going on. Make sure you've properly > re-imaged to account for PBC effects. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.