From: Robert Brunner (rbrunner_at_uiuc.edu)
Date: Tue May 10 2005 - 11:41:37 CDT
Some factors in MD are already space-like. Gravity is not simulated
in NAMD, so essentially you already have zero-g. NAMD also does not
provide you an atmosphere; you have to supply that yourself by
filling space with explicit water molecules. Leave those out, and you
have a vacuum simulation. Temperature is a variable that is
determined by how you set up and equilibrate your simulation, so high
temperature is also easily achieved (if the molecules you're
simulating don't fly apart at high temps). Radiation is about the
only factor that wouldn't be part of a normal simulation. I don't
think that would be well-handled by classical MD, since radiation
effects like ionization tend to work at the quantum level.
I'm not a physicist, but there's my 2 cents.
On May 6, 2005, at 1:20 PM, Gaurav Sharma wrote:
> Hi All,
> My objective is to study the effect of space-like conditions on the
> struture and functions of a protein. So my question is :
> Is there any way we can simulate a protein in a 'space like'
> environment using MD. By 'space like', I mean environments such as
> micro gravity, high vacuum., radiation filled or extreme
> temperature conditions. But a part of this question also involves
> seeking a better understanding of what can be an ideal space-like
> environment with regards to Molecular dynamics. Is it possible to
> replace water with some other solvent which is better suited for
> simulating space like MD ?
> Any advice would be appreciated.
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