On 4/4/13 2:14 AM, rama david wrote:
Dear Friends,
I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.
Now I want to draw the Free energy surface for the
same ..How is there pot energy ???
Would you please tell me how to do it ..
( I read about g_sham -h, I tried it, but not understand properly)
I will be very grateful for your suggestion and help..
The logic behind g_sham was just posted to this list no more than a few days
ago.
http://lists.gromacs.org/pipermail/gmx-users/2013-March/079810.html
It calculates a free energy surface as a function of two variables of your
choosing. As David noted
(http://lists.gromacs.org/pipermail/gmx-users/2013-March/079813.html), the
result may not correspond to a true quantitative representation of free energy
differences, though.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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