[gmx-users] Force Field for Vacuum simulation

[Peter C. Lai]

On 2012-02-02 04:46:03PM +0300, James Starlight wrote:
> Peter,
> 
> thank you it's very intresting survey. I'll try to investigate it
> carefully. I've looking for the same issue for along time it's also would
> be good to find more recent review on the same topic.
> 
> By the way today I've found that the testing on the receptor stability in
> the case of some point mutations might not be good with the unbiassed MD
> simulation. Some people told me that for most valid result the biased MD by
> the aplication of the external forces must be done.  Finally even if i've
> done very 'deadly' mutation (e.g strong perturbation of the tight packing
> in the functional-relevant region of the transmembrane segment) this effect
> could not been seen even in the relatively long trajectory.

Maybe. What was substituted? I mean if you start putting in lysines or
arginines along the TM regions where there are supposed to closely packed
nonpolar residues I would expect to see a bunch of effects within 10-50ns...

You can apply external forces to your system in gromacs through the use
of pulling in order to calculate PMF. (see manual) see also 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

> 
> By contract that publication wich you provide the different conditions were
> tested for the refirement of the X-ray result in the standart MD.
> 
> So is there any compromise between both of the methods of the MD?

Sorry I don't understand the question here (compromise between both of the 
methods?)
I mentioned the refence to give you an idea that "not all hydrophobic 
enviroments behave the same" when it comes to interacting with the protein...
You will have to judge how much of that paper specifically applies to your
individual case...

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