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

[Justin Lemkul]

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

-- 
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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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