Thank you Your advice is very helpful I will try to reparametrize the molecule, which I think is a better strategy.
On Sun, Oct 6, 2019 at 6:38 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/5/19 1:58 PM, Quin K wrote: > > 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? > > I imagine it's possible that the power failure caused a corruption in > some file, and it's too much of a coincidence that just when the power > failed, your simulation changed radically. I would re-run it. > > Also note that a ligand can dissociate from the binding site if the > topology is not well parametrized, leading to insufficiently strong > interactions. You shouldn't likely encounter such a problem if you get a > reasonable CGenFF topology, but it's worth noting as a general problem > with any ligand parametrization. > > -Justin > > > 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. > >> > > -- > ================================================== > > 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.