Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My question is-
1. while calculating radial distribution functions say between DNA minor groove and choline, should I consider the center-off-mass atom of the minor groove by using the -COM option of g_rdf? 2. Do you think calculation of PMF from g(r) for a specific ion binding with the DNA can provide reliable free energy change or do I have to switch to umbrella sampling? PS: I only want to investigate the small molecule binding, not the stability of the DNA duplex as a whole. Thanks for your time in advance. Soumadwip Ghosh Research Fellow Indian Institute of Technology Bombay 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.