[gmx-users] Umbrella sampling for protein-drug system

Aldo Segura asegurac666 at yahoo.com.mx
Sun Feb 20 07:34:03 CET 2011

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: asegurac at ipn.mxaldosegura at gmail.com

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