[gmx-users] cut-off

[Justin Lemkul]

On 6/18/15 7:47 AM, Faezeh Pousaneh wrote:
> Thanks Justin.
>
> yes, you are right, my simulation is very sensitive to cut-off.
>
> I did not understand what do you meant by '' is the balance of forces
> correct''?
>

For this you should read about how force fields are derived.  Far too extensive 
of a topic for email, sorry.

> So If I understood you correctly, the cut-off lengths must be chosen from
> the force filed, yes?

Yes.

> Since I am not expert how to choose a force field, could you tell me a
> proper force field for Benzene all-atom model?
>

Try a few; see which one reproduces its physical properties best for whatever 
your intended purposes are.  No model perfectly captures everything.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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