Re: [AMBER] potential energy

From: Carlos Simmerling <>
Date: Fri, 13 Jan 2017 06:35:26 -0500

The first step would be to place error bars on your energies to estimate
precision. Unless you want to know the energies of specific
conformations,you will need to make sure you have appropriately sampled the
distribution. This can be difficult for constrained peptides. Simple
approaches such as first vs second half of md are probably going to
underestimate the error. Once you have assured the convergence of the
sampling, you can start to compare the energies. Depending on peptide
length, you may end up needing enhanced sampling methods. There are many
studies in the literature that go into more detail than is possible here on
the email list.

On Jan 13, 2017 6:16 AM, "Albert" <> wrote:

> It is a cyclic peptide. One is in R conformation, the other one is in S
> conformation.
> I want to figure out which conformation is more favourable from the
> aspect of potential energy.....
> On 01/13/2017 12:14 PM, Carlos Simmerling wrote:
> > Can you say more about what you mean by stable? Do they have a folded
> > structure that unfolds? Or do you mean is R preferred over S?
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Received on Fri Jan 13 2017 - 04:00:02 PST
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