[gmx-users] About Free energy surface .....g_sas

Justin Lemkul jalemkul at vt.edu
Thu Apr 4 10:26:48 CEST 2013

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.


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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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