**From:** Aaron Larsen (*alarsen_at_molbio.mgh.harvard.edu*)

**Date:** Mon Feb 03 2014 - 13:32:45 CST

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Hello,

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

system.

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.

Best,

Aaron

**Next message:**Dan F. X. Martingano: "Re: Umbrella Sampling of Sugar Pseudorotation"**Previous message:**zeynab mohamad hoseyni: "Hydration of protein-lipid interface"**Next in thread:**Dan F. X. Martingano: "Re: Umbrella Sampling of Sugar Pseudorotation"**Reply:**Dan F. X. Martingano: "Re: Umbrella Sampling of Sugar Pseudorotation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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