Hello Tasneem, Same like you, I'm pretty new to this field too. I don't know enough how to calculate free energy in gromacs. I did only MM/PBSA for binding energy calculations. I'll let you know if i get some thing relevant to your question.
All the best. Thanks On Thu, Jan 5, 2017 at 10:28 PM, tasneem kausar <tasneemkausa...@gmail.com> wrote: > Dear all > > It is first time I am calculating free energy of protein and ligand. I am > following the Justin's tutorial of methane in water free energy > calculations. Though only van der waal lambda are defined so I have taken > the mdp files from the alchemistry.org web page. Since the ligand and > protein under my study have positive charges (one positive charge on ligand > and tree positive charges on protein). So I have to add a CL ions in > topology file to make a neutral sytem. > Is it okay to use the system with ion for free energy calculation? > If yes, What are change that can be made in mdp entry. > > Waiting for suggestions > Thanks in Advance > -- > 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. > -- 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.