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

[Justin Lemkul]

On 7/24/14, 4:30 PM, Elton Carvalho wrote:
> 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
> well.
>

The definition of sigma is always the same; the issue is whether or not force 
fields specify sigma directly or Rmin/2, etc.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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