Hello: I am new to GROMACS.
I would like to run ligand-protein absolute FEP simulations with GROMACS-CHARMM36 ff. My aim is to compare with the same simulations I carried out with NAMD-CHARMM36 ff. I got the .top file inclusive of all parametrss via TOPOGROMACS. I plan to obtain all necessary files to first continue MD equilibrations with GROMACS by passing the NAMD equilibrated .pdb file and the .top file to GROMPP (I am looking for direction on howto). The thermodynamic cycle I used with NAMD is similar to the one in the 2016 GROMACS FEP tutorial. However, I am rather confused on how to add flags and restraints after the MD equilibration. With NAMD, FEP flags and restraints are simply added to the general MD configuration file. Thanks for advice. francesco pietra -- 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.