From: McGuire, Kelly (
Date: Thu May 24 2018 - 12:10:34 CDT

I am preparing to do some ABF calculations with the molecules I sent through FFTK by working through the tutorial. I am placing these molecules in the influenza A M2 protein to get their free energy profiles in order to understand their entry/exit and interactions inside the protein. I will have some questions as I work my way through the tutorial. My first one is more of a general question on how ABF works. I've done some umbrella sampling before, and the way we have done this in the past is create multiple input files with the molecule/drug at different positions in the protein, delete the waters at the drugs new position, and submit all of those jobs to the supercomputer, which as you can imagine is very tedious/inefficient. I am wondering though how the ABF set up in NAMD handles moving the drug and deleting waters around the drug at the new position? For example, say I have the drug starting at one end of the protein and we call that position on the reaction coordinate -15 Angstroms, and the drug is to be moved to the other end of the protein, call it 15 angstroms (so, 30 angstroms for the total reaction coordinate), how does the part of the colvars script, (width 0.1, lowerboundary -15, upperboundary 15), move the drug to the next spot and delete waters around it? Is this some kind of a loop that NAMD recognizes to move the drug? Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602