[gmx-users] Re: Umbrella sampling and free energy estimation

[James Starlight]

Restating of my question about ussage of essential eigenvectors as the
pulling coordinates I'd like to introduce some example.
The case study is the open to close transition in some protein. For
instance by means of essential dynamics sampling technique (in
targeted-contraction mode) I've simulated transition from open to
close state of my protein (obtaining 1ns trajectory where such process
can be visualized). Could I use such trajectory for further umbrella
sampling of my protein ussing conformers extracted from that 1ns
trajectory as the umbrella\s windows (analysing them by means of WHAM
method).


James

2013/1/15 James Starlight <jmsstarlight at gmail.com>:
> Dear Gromacs Users!
>
>
> Recently I've completed Umbrella sampling tutorial presented on the
> Justin's web. I'd like to use that teqnique as the engine for
> enhansing of conformational sampling of some monomeric proteins
> (starting with the simplest example of apo-calmodulin) as well as
> estimation of the free energy of apo form of my protein ( something
> like free energy surface)/ So I have some methodolofical questrions
> about emplementration of the umbrella sampling to the  such tasks.
> 1- Does it possible to obtain representation of the distribution of
> conformational free energy of my protein by means of that method ? (
> estimation of what conformations are most hightly-populated from
> overal protein ensemble )
>
> 2- Also I wounder to know about pulling algorithm. Might I use some
> eigenvector (or the combination of selected eigenvectors) extracted by
> the covariance analysis of the equiliubrium trajectory or by the PCA
> from the experimental data-set of the simulated protein ?
> What changes to the pulling algorithm should I add for such simulation?
> Also I found in that settings 2 groups- where  pull_group1  is what
> I'd like to pull.
> pull_group0     = Chain_B
> pull_group1     = Chain_A
>
>  If I have just one group ( protein itself) which I'd like to pujll
> along selected coordinate what I should specify as reference
> (pull_group0) ?
>
>
> Thanks for help,
>
>
> James