What Gibbs energy are you trying to calculate for the system? Of what process or transformation?
On Wed, 29 Aug. 2018, 3:56 pm abhisek Mondal, <abhisek.m...@gmail.com> wrote: > Hi, > I'm just trying to calculate free energy of a complex system using > following method: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html > > However, I'm facing some difficulties understanding how can I achieve the > goal. The tutorial goes on with a single entity from lambda=0 to 1 with > 0.05 spacing for data collection. > > Now, if I would like to calculate free energy of a complex (say, dimeric > protein) then how am I supposed to design the lambda states ? > I mean will it be like, one monomer will remain constant and the other > monomer goes from lambda=0 to 1 state ? If that be the case then please > suggest a way to customize the procedure. > > Please provide some suggestions. > I'm really willing to apply this method in my scenario. > Thank you. > -- > Abhisek Mondal > > *Senior Research Fellow* > *Protein Crystallography Group* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *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. > -- 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.