[gmx-users] questions in Running MDS over docked poses

[Justin A. Lemkul]

vivek sharma wrote:
> hi Justin,
> Thanks for your reply...
> I am interested in looking for the stability of the docked pose, by 
> applying some temperature variation in the molecule.
> If I am applying temperature variation then should I use pressure 
> coupling simultaneously.

Well that's going to depend on how much you're varying the temperature.  I have 
a colleague who has done some thermal stability simulations upwards of 600K and 
the NPT algorithm breaks down (using AMBER).  I don't know if that's true of the 
Gromacs code as well.

> Can you suggest some tutorial for such attempts.....
>

Well, I don't know about tutorials, but (again depending on how much you're 
varying the temperature) some of the literature regarding thermal stability of 
proteins over wide temperature ranges might be of interest.

-Justin

> With Thanks,
> Vivek
> 
> 2008/11/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         Hi There,
>         I am running MDS over the docked poses to check the stability of
>         the docked poses using gromacs.
>         I have few doubts about selecting parameters for the same, If
>         anybody have tried such thing earlier, please suggest me for the
>         same.
> 
>         Should I keep pressure coupling over the simulation ?
> 
> 
>     Sure; life exists at NPT, so it is commonly used in routine protein
>     simulations.
> 
> 
>         For how long should I run the simulation for such purpose ?
> 
> 
>     That's up to you :)  You should run the simulations as long as you
>     feel necessary to achieve stability.  I know that's vague, but there
>     really is no single correct answer to this question in the MD field.
>      If there is, I'd love for someone to tell me, too...;)
> 
>     -Justin
> 
>         Waiting for suggestions.
> 
>         With Thanks,
>         Vivek
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================