Hi Mark.

thanks a lot for your comments.

These two peptides are isomers.

I want to know which conformations is more favourable than the other from the aspect of potential energy.....

However, the system potential energy and the peptide potential energy seems to be inconsistent with each other.... So I am pretty confused right now....


On 01/13/2017 12:16 PM, Mark Abraham wrote:

Having low potential energy (whether in dynamical simulation or em) and
being (any kind of) stable are nearly unrelated concepts. There may be a
way to measure what you want, but so far I suspect you haven't worked out a
good way to describe what you want.

Further, unless your peptides are isomers, your potential energies are of
systems with different composition, so can't be compared.


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