[gmx-users] about potential energy calculation

[Mark Abraham]

Hi,

On Fri, Jan 13, 2017 at 12:20 PM Albert <mailmd2011 at gmail.com> wrote:

> 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.....
>

But that doesn't tell anybody anything. A low-energy state might be a high
entropy state. You sound like you want to observe a free-energy difference.


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

There's no reason to expect consistency. Replacing a hydrogen bond to water
by an internal one through changing conformation will change the PE of the
peptide, the water and total, each by different amounts. The thing that
matters is the relative frequencies of the conformations, but the PE
doesn't tell you that.

Mark

regards
>
>
>
> 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
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>