[gmx-users] Force Field for Vacuum simulation

[Peter C. Lai]

On 2012-02-03 08:46:25AM +0300, James Starlight wrote:
> Peter,
> 
> 1- Yes I've also found that the umbrella simulation is exactly that I need.
> Now I'm studing this tutorial more carefully.
> 
> 
> 2- In other words my second question was: in what exactly situations ( e.g
> some kind of point mutation) the unbiassed MD may be enought to detect
> unstability of the system (one of that examples you've already mentioned
> with the Lys Arg substitutions in TM region ) and in what cases the biassed
> MD (e.g the PMF) may be needed?

Depends on what you want to measure and demonstrate. It may be sufficient
just to look at different rates of RMSD changes or distance changes, 
particularly because we are still looking at intra-molecular interactions
(even though the interactions are tertiary). But then again, some people
might feel that ddG measurements are better suited for their narrative.

Maybe start looking at what the protein folding people are doing too, 
since they also use the point mutation technique to probe stability and 
transition states through various stages of (un)folding...

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