From: Dan F. X. Martingano (Dynamic00_at_msn.com)
Date: Mon Feb 03 2014 - 13:40:08 CST
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> On Feb 3, 2014, at 2:36 PM, "Aaron Larsen" <alarsen_at_molbio.mgh.harvard.edu> wrote:
>
> 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
>
>
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