[gmx-users] Re: Help

[Justin A. Lemkul]

vivek sharma wrote:
> HI justin,
> Thanks for reply. It is well understood that the energy minimization 
> step will minimize energy, but what is the purpose of MD (after EM and PR)?
> please reply

Again, please keep all Gromacs-related correspondence on the gmx-users list.

The purpose of MD?  Integrating Newton's Laws of Motion across the contents of 
an atomic-scale system.  As for what you want to do with it, that is up to you. 
  Check the literature for what people are doing with MD if you are unsure 
(i.e., have a look at any recent issue of Biophysical Journal or any number of 
others).

-Justin

> 
> With Thanks,
> Vivek
> 
> 2008/8/27 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         Hi Justin,
>         I think my query is very basic regarding GROMACS, so I am
>         mailing you individually instead of using mailing list.
> 
> 
>     Basic or not, please keep all Gromacs-related correspondence on the
>     gmx-users list.
> 
> 
>         My query is ...
>         How does gromacs proceed ?
>         On what basis (parameters) it decides the next frame ?
> 
> 
>     Read about the algorithm in the manual.
> 
> 
>         and, what is the target of trajectory means where it is leading
>         to ? is it energy minimization or something else.
> 
> 
>     The target of the trajectory is whatever is of interest.  As for
>     whether or not you can force that to happen...
> 
>     "Energy minimization," strictly speaking, is a preparatory step that
>     attempts to remove bad contacts from the system.  In a sense, one
>     can think of natural phenomena as seeking a global energy minimum,
>     which is what we would like to see happen in many cases.
> 
>     -Justin
> 
> 
> 
>         I am from an engineering background.
> 
> 
>         With Thanks,
>         Vivek
> 
> 
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
> 
> 

-- 
========================================

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

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