Thanks Justin as always for your prompt reply. I have now created the graphene topology the way u suggested that is I issued the following command
1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the -noparam option since it does not print the k0, k1 and similar values. 2. I have now started the simulation with all my mdp files (ions.mdp, minim.mdp, nvt.mdp, npt.mdp and md.mdp) containing the "periodic molecules=yes" line and as of now the simulation is running fine. But the last one crashed around 25 ns showing the Lincs warnings and stuffs so keeping my fingers crossed. 3. I am keeping the dihedral function type 1 as per your suggestion. Please let me know if what I am doing right now as mentioned above makes sense or not. I will update on the outcomes of my simulation even if everything goes right. Thanks once again for the reply Justin..:) Soumadwip Ghosh Senior Research Fellow Indian Institute of Technology Bombay India -- 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.
