Dear all, I am trying to study wetting of Graphene oxide. I have prepared a structure file using material studio, which I will simulate in GROMACS.
My structure contain some epoxy and hydroxyl functional group in Graphene sheet. However, the structure file generated does not differentiate between carbon atoms with and without functional group in the "Name" column of .pdb file. Also there is no differentiation in naming format of oxygen atom in epoxy and hydroxyl group. Since, these atoms will have different atom type in atomtype.atp file of force filed.(I will be using OPLS-AA for simulation). Do I have to make edits in .pdb file for different atomtypes as well. Thanks Rajan Kumar Department of Chemical Engineering Indian Institute of Technology, Guwahati -- 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.
