[gmx-users] cut-off

[Faezeh Pousaneh]

Thank you Justin,


Best regards


On Fri, Jun 19, 2015 at 2:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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