Molecular Dynamics Simulations, NVT & NVE

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Molecular Dynamics Simulations, NVT & NVE

Postby BioWizard on November 7th, 2010, 2:47 am 

Is anyone aware of all the details and considerations regarding whether to use NVT or NVE ensembles in a MD simulation? (NVE : adiabetic, NVT: constant volume and temperature).

I'm doing a MD simulation to follow the trajectory of an amino acid side chain after I mutate it from a hydrophilic to a hydrophobic residue. My biochemical intuition tells me that in solution, the residue probably rotates so that the hydrophobic side chain can pack against a nearby hydrophobic pocket (which is an entropic effect). I'm inclined to use NVT, but I can't solidly defend that choice. Thoughts?
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Re: Molecular Dynamics Simulations, NVT & NVE

Postby neuro on November 8th, 2010, 5:39 pm 

My impression is that you may well get a maximum enthropy solution via both methods, but if you are interested in the trajectory, then as you say it would be preferable to use NVT, because the trajectory would be pretty much interfered by momentary changes in temperature which occur in the simulation (if you use NVE) in an exaggerated way w.r.t. what is supposed to occur in solution and with a high number of molecules (which all contribute to absorb/release the heat your conformational change would release/absorb).

my 2 cents
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Re: Molecular Dynamics Simulations, NVT & NVE

Postby BioWizard on November 8th, 2010, 7:46 pm 

Neuro, that's what I thought too.

I should've been clear that what I'm trying to do here is simulated annealing. I'm increasing the temperature of my system gradually over several MD steps (298 to 330), and then bringing it down back to 298, in the hope to see what will happen to the orientation of the loop when the hydrophilic residue is replaced by a hydrophic one. So it's not the trajectory I'm interested inasmuch as any conformational convergence.
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