[gmx-users] about potential energy calculation

[Anders Støttrup Larsen]

Do you have the same amount of molecules in each simulation?

Anders

On Fri, Jan 13, 2017 at 12:19 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.....
>
> However, the system potential energy and the peptide potential energy
> seems to be inconsistent with each other.... So I am pretty confused right
> now....
>
> 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
>>
>
>
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