Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial.
I also wanted to ask that while create special index groups consisting of solvent + ions and protein + lipids using make_ndx if i am having a system with ligand molecule also then should I add it with protein lipid complex or add it separately with protein like 16 | 14" to merge the SOL and CL groups "1 | 13 |" to merge Protein and POPC groups and 1 | 12 to merge Protein and LIGAND groups or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC groups With Regards Neha bharty -- 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.
