Dear gmx-users, I have following the umbrella sampling tutorial at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html. I’m trying to use it for a drug-protein system. In the tutorial the group A moves away to group B. I would like to pull the drug to the protein binding-site (i.e., drug move closer to protein). How can I do that? Should I modified the md_pull.mdp file (from the tutorial) changing the value from pull_rate1 (0.01) to a negative value (i.e. -0.01)? or using pull_geometry = position and related code instead pull_geometry = distance?
Thanks in advance, ======================================= Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: [email protected]; [email protected] =========================================
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