[gmx-users] Coulomb-14 Energy
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 25 07:04:22 CEST 2018
Den 2018-04-24 kl. 15:49, skrev Mark Abraham:
> There is no physical meaning to this decomposition. There is nothing to
> The total energies are different for each system, too. How would you
> justify that? They're just different systems with different compositions.
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.
> 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
>> Zaved Hazarika
>> PhD Scholar
>> Dept.of Molecular Biology and Biotechnology
>> Tezpur University
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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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