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

[Elton Carvalho]

On Thu, Jul 24, 2014 at 10:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> On 7/24/14, 4:30 PM, Elton Carvalho wrote:
>>
>> 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
>> well.
>>
>
> The definition of sigma is always the same; the issue is whether or not
> force fields specify sigma directly or Rmin/2, etc.
>

I stand corrected. sigma is well defined. The point is wether the
"distance parameter" in the LJ formula is sigma or the minimum, or
half the minimum etc. As an example, Accelrys' Cerius2 (and Materials

Studio too, AFIK), define Lennard-Jones as (according to its
documentation):

     LJ 12 6:       E = Do { ( Ro/R )^12 - 2 * ( Ro/R )^6 }

                    Do - Well depth in kcal/mol
                    Ro - Equilibrium distance in Angstroms

This was exactly the scenario I had trouble with: trying to implement
a Cerius2 forcefield in gromacs.

Either way, checking what the "distance parameter" means in the
forcefield the user is trying to reproduce is a nice to place to start
if he is experiencing this kind of discrepancy.

Cheers from a windy, chilly Curitiba.

-- 
Elton Carvalho
Departamento de Física
Universidade Federal do Paraná

Departamento de Física
Universidade Federal do Paraná