Hi, On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan <ashmakhan...@gmail.com> wrote:
> Thank you for your suggestion Alessandra Villa > I have applied all types of pbc conditions but my one peptide is diffusing > away from another peptide in case of dimer after half of the simulation > time and rmsd is coming out 100 Angstrom after that time which is very > high. Please suggest me what should I do. > When you visualize the trajectory (for example in VMD), you see the dimer breaking and the two peptides moving apart inside the box (in a "continuous" way and not jumping in and out the box or moving out of the box). That probably means that in your simulation condition, the two peptides do not form a dimer. Best regards Alessandra > -- > Ashma Khan > Research Scholar > Department of Chemistry > AMU, Aligarh > -- > 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.