Dear Justin, Thank you for your kind response.
I have made all the basic analysis and yes there are certain structural changes that i have expected. But my clarification is as follows. Initially, there were 6 H-bonds and when it reach around 15ns it is reduced to 1 or 2. Do the effect of ligand over protein increase/decrease with a number of hydrogen bonds? Or even a single bond between protein and ligand is more sufficient to bring necessary changes to a protein? With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- 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.
