[gmx-users] about potential energy calculation

Albert mailmd2011 at gmail.com
Fri Jan 13 12:20:01 CET 2017

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:
> Hi,
> 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.
> Mark

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