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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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
========================================
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