Re: accelerated MD as the engine for loop refirement

From: Gianluca Interlandi (
Date: Wed Jul 09 2014 - 15:08:17 CDT

Accelerated MD + implicit solvent. In my opinion, that might cause too
many distortions. It's a good start to get an idea of the accessible phase
space but whether that will really tell you the most likely conformation
nobody can say for sure. I would use regular MD in explicit solvent
coupled with something like REM. But that is just my 2c.

A good start would be to simply run two MD simulations in explicit water
at 300 and/or 310 K (50 - 100 ns) and see what those loops do.


On Wed, 9 Jul 2014, James Starlight wrote:

> Dear NAMD users!
> I wounder whether the accelerated molecular dynamics might be good solution for the
> loop refirement of models made by means of hoology modeling with the teplated which
> has the low sequence identify in loop region? For instance I've just built some
> models of membrane receptors agains receptor with known structures and would like to
> refine loops by some enhansed sampling engine to sample all possible conformation and
> found most propable during short simulation. Does the acceleraed md good sollution
> for such task assuming simulation with implicit solvent with restrained all atoms of
> the helix regions of the refined protein but not loops flexible region? What
> alternatives should I explored also?
> TFH,
> James

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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