[gmx-users] Cyclohexane simulation problem

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 5/30/15 8:44 AM, mohsen shahlaei wrote:
> Dear Justin,
> Thanks, could you please explain what is difference between Cut-off and PME in
> calculation of electrostatic interactions
>

Simply, a cutoff is what it says it is - a plain truncation at a finite 
distance.  For electrostatics, this is very crude and shouldn't be used in 
modern simulations.  For your system, which has no charges, it doesn't matter. 
PME takes long-range interactions into account.  The full description of PME and 
why people generally use it is way beyond what I'm will to type out, so suffice 
it to say you should be reading the description of the algorithm in the manual 
and the citations provided therein.

-Justin

-- 
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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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