Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file?
Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT <https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing> I am not continuing any of the equilibration steps anymore. As you can see the CNT structure is distorted badly. Please help me out. What settings do I need to change in order to avoid such distortion? Is there a possibility that the cnt topology was wrong to begin with? Regards, Soumadwip Research Fellow IITB 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.
