Dear Justin, My previous problem was solved after I used all-bonds instead of hbonds in constraint section of mdp file. (I got the topology for my ligand using antechamber).
After completion of NVT equilibration phase, I viewed nvt.gro using vmd. Please see the related figure in the following link: https://www.dropbox.com/s/i3ezsacp5jxotin/figure.png?dl=0 What is the reason of this problem and how to resolve that? Any help will highly appreciated. -- 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.
