[gmx-users] Doubts in combination rules 2 and 3

Mark Abraham mark.j.abraham at gmail.com
Tue Jun 12 10:28:12 CEST 2018


You'll learn a lot more, and have confidence that you are getting what you
want, if you make a tiny system in vacuum, so you can observe how changes
in your topology propagate through grompp into your .tpr file. Use gmx dump
-s to see.


On Tue, Jun 12, 2018 at 10:25 AM Apramita Chand <apramita.chand at gmail.com>

> Dear Justin and David,
> Thanks for your replies. So as I understand from your answers, I need to
> put the sigma and epsilon for my atomtypes (without any conversions) under
> the C6 and C12 columns in ffnonbonded.itp  and these numbers will be
> interpreted as sigma and epsilon when I specify the combination number.
> Also, I don't need to add anything in the non-bonded params section, the
> interactions will be automatically calculated.
> Please correct me if I'm wrong.
> Thanking you,
> Yours sincerely,
> Apramita
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