Umbrella Sampling of Sugar Pseudorotation

From: Aaron Larsen (
Date: Mon Feb 03 2014 - 13:32:45 CST


I have recently performed equilibrium calculations on short
oligonucleotides to investigate factors influencing the pseudorotation of
the sugar pucker. I would like to extend this work to include Umbrella
sampling to establish the energy landscape along this coordinate.

There have been some similar questions asked here but none seem to apply
very directly to my situation.

First, I would like to establish that I have the correct notion as to the
steps involved in this process.

1) Generate a series of coordinates for a given system along the chosen
reaction coordinate. In my case, this would be a nucleotide with different
values, P, for the sugar pucker.

2) For each set of coordinates, apply a restraint and then minimize the

3) For each system. apply a specific energy in a particular direction and
record the resulting trajectories.

4) Compile the trajectory files and use WHAM to investigate the PMF along
the chosen coordinate.

Assuming that this is correct, is there any tutorial that can get me
started on this process? I was unable to find reference to Umbrella
sampling in the tutorial on the webpage but it might be covered by a
different term.


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