[gmx-users] Lennrd-Jones potential in Gromos force field

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 13 14:55:10 CEST 2018


All force fields have functional forms and parameters for them that have
been arbitrarily and empirically determined in ways that they reproduce
some observables. Except if the designers intended some component to have a
physical interpretation, there is none you should make without clear
evidence that it works. That's because all the components  are mutually
compensating for deficiencies of the others. When you read up on the force
field you are using, you will probably learn that there is no such intent
or evidence for the gromos force fields. A free energy of binding could be
meaningful, however.


On Wed, Jun 13, 2018, 12:34 <kordzadeh at aut.ac.ir> wrote:

> ​Hi all
> I've simulated interaction of functionalized carbon nanotubes with drug
> with Gromos 54a7 force field, by gmx energy module and defining enegy grps
> I obtained LJ-SR , short range Lennad-jones potential between drug and CNT,
> in my system there are different interavtions, polar-polar,
> nonpolar-nonpolar, vdw,...
> I have a question, what does interaction include in LJ option in gmx
> energy module, (polar, nonpolar,vdw..) ?
> I think LJ equation is a equation with some parts, such as: attarction,
> repulsion, polar and..., Does Gromos consider polarity in LJ equation or it
> has only attraction and repulsion,
> if it has attraction and repulsion what can I call the output from gmx
> energy, can I call it vdw,?
> what focefiald can consider polarity?
> any suggestion will be appreciated
> Thanks
> Regards
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