From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Jul 10 2014 - 17:59:24 CDT
Why not just running accelerated MD and explicit solvent? That might
already confer an idea of the flexibility of the loops. Another
alternative is to use metadynamics (implemented as COLVARS in NAMD or
through the plumed plugin) and explicit water. Metadynamics should be more
efficient than accelerated MD once you have identified the correct collect
variables.
You can also try out implicit solvent on its own or couple it with REM.
But I would always test those things independently before combining them.
Gianluca
On Thu, 10 Jul 2014, Kenno Vanommeslaeghe wrote:
> It all depends. These loops often require very long timescales to get descent
> sampling, such that the sampling error when using explicit solvent might be
> greater than the error in the implicit solvent energetics. Though I have no
> idea whether there's any specific crosstalk between Accelerated MD and
> implicit solvent (my guess would be "no" but that's just a guess).
>
>
> On 07/09/2014 04:08 PM, Gianluca Interlandi wrote:
>> 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.
>>
>> Gianluca
>>
>> 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 gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Research Assistant Professor at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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