[gmx-users] Comparing different conformations of a polypeptide

[Erik Marklund]

Hi,

I guess you want to compare the relevant free energies for the ensemble 
in question. There are plenty of free energy methods around, most of 
them fairly complicated. If you sample conformational space enough by 
brute force simulations, you can get the relative free energies for any 
two states from how often they appear in the trajectory. Now, go and 
brush up your statistical mechanics and thermodynamics!

/Erik

nur avneet skrev:
>
>
>     Dear All
>      
>     I have run different conformations of a polypeptide in spc water
>     for 1ns, keeping the box size, volume and no. of water molecules same.
>     Can i compare the enrgies of the different conformations after
>     simulation and on its basis say which one of them is stable.
>     also, to see the conformation in its most stable form can i take
>     that time point when the energy was minimum?
>      
>     regards
>     nur
>
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys