[gmx-users] Cohesive Energy Density (CED) Calculation in Gromacs simulations
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 1 08:34:47 CET 2017
On 01/03/17 07:30, ZUO Taisen wrote:
> Hi guys:
> Recently, I'm simulation a protein in the mixture of water and ethanol. And I want to know the interaction energy among the three items and also the Cohesive Energy Density of the whole system.
Never old enough to learn something new, I had never heard of Cohesive
Energy Density but I found this:
this parameter has a non-physical unit of sqrt(kg/m)/s
It is important to realize that this kind of chemical engineering
properties do not have any fundamental information, although they may be
Interaction energy is only a valid concept in the limit of pure pair
potentials, which is what we use in classical non-polarizable
simulations (but in e.g. quantum chemistry there is no real equivalent).
You can decompose the reciprocal part of the Coulomb energy according to
the supporting information of
If you want to study a more meaningful property like the enthalpy of
mixing you would have to do a concentration series, like here:
> In order to calculate the cohesive energy I only added up LJ (SR) Disper. corr. Coulomb (SR) and Coul. recip. from the log file of Gromacs. But someone pointed out that Disper. corr.and Coul. recip.are correction of cutoff of the nonbonded interaction namely LJ and Coulomb interaction.It also contain the energy inside the molecules namely long range correction of LJ-14 and Coulomb-14。I don't know whether he is correct or not, but I can never find anywhere a lenthy description of the Disper. corr.and Coul. recip. in the manual of Gromacs.
> Could soneone explain the meaning of Disper. corr.and Coul. recip. and offer me the methods of calculating the correct CED of the system and individual interaction energy like Protein-SOL and SOL-SOL?
> Taisen Zuo
> China Spallation Neutron Source，Institute of High Energy Physics， Chinese Academy of Science
> A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
> Tel: 86-0769-89156495
> Cell: 13650469795
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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