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
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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