[gmx-users] Lennard-Jones potential not matching with published data

Elton Carvalho eltonfc at if.usp.br
Thu Jul 24 22:39:27 CEST 2014

On Wed, Jul 23, 2014 at 3:40 PM, ibrahim khalil
<ibrahim.khalil.chem at gmail.com> wrote:
> In my simulation, my results are about half (not exactly half but around
> half) of the published data. I am stuck here for like a month and cannot
> find my mistakes.
> Can anyone help me where to look for my mistake? I am using a modified
> oplsaa forcefield.
> Should i check my forcefield parameters? Or my mdp parameters?

I've been there before.

Check which Lennard-Jones function was used to publish the data to
which you are comparing. There are some nomenclature differences
regarding sigma. GROAMCS defines sigma as the distance where the LJ
potential is zero. Some forcefields define sigma as the bottom of the

Checking wether your reference uses 6-12 or 6-9 LJ funcions may also help.

Elton Carvalho
Departamento de Física
Universidade Federal do Paraná

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