[gmx-users] Re: Help

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 27 11:51:18 CEST 2008

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.


> 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 | (540) 231-9080


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