[gmx-users] Comparing different conformations of a polypeptide

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 19 14:40:19 CET 2010

It also depends on what you meen by 'stable'. If it refers to lowest 
potential energy, then you can just find the minimum from the edr-file. 
Such a conformation may not make any chemical sense though. Could you be 
more precise?


Erik Marklund skrev:
> 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

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