[gmx-users] Coulomb-14 Energy

zaved at tezu.ernet.in zaved at tezu.ernet.in
Thu Apr 26 12:28:19 CEST 2018


Thank you Mark and David for your kind responses.

> Den 2018-04-24 kl. 15:49, skrev Mark Abraham:
>> Hi,
>>
>> There is no physical meaning to this decomposition. There is nothing to
>> justify.
>>
>> The total energies are different for each system, too. How would you
>> justify that? They're just different systems with different
>> compositions.
>>

I was thinking on the same line.

Just wondering then why am I getting identical C-14 value in case of water
and urea?

Further does it mean that all other energy values except total has no
meaning at all?

Thank You


>
> The 1-4 energy has intramolecular contributions from the solvent as well
> if it is larger than water. This is probably what you are seeing.
>
> Other than that Mark is right, there is only one energy.
>
>> Mark
>>
>> On Tue, Apr 24, 2018 at 1:35 PM <zaved at tezu.ernet.in> wrote:
>>
>>> Dear Gromacs Users
>>>
>>> I have simulated a protein in presence of GdmCl (1519 Gdm and 1519 Cl)
>>> and
>>> Urea (urea 1843) with gromos54a7 ff for 100ns each.
>>>
>>> The Average Coulomb-14 Energies of protein in water, urea and GdmCl
>>> are:
>>> 3.42E+04, 3.41E+04 and -3.16E+06 respectively.
>>>
>>> The value of Coulomb-14 in case of protein in presence of water and
>>> protein in presence of urea are almost identical whereas it tends to be
>>> in
>>> different in case of GdmCl. And inspite of the fact that both urea and
>>> GdmCl have negative potential.
>>>
>>> How do we justify this?
>>>
>>> Thank You
>>>
>>> Regards
>>> Zaved Hazarika
>>> PhD Scholar
>>> Dept.of Molecular Biology and Biotechnology
>>> Tezpur University
>>> India
>>>
>>>
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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