[gmx-users] Justin tutorial - V-rescale + Parinello-Rahman

[Steven Neumann]

Thank you for this!

Steven


On Wed, Apr 9, 2014 at 2:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/9/14, 8:18 AM, Steven Neumann wrote:
>
>> Dear Gmx Users, Dear Justin
>>
>> I have noticed that in in our tutorial(s) in thew mdp option you
>> suggesting
>> V-rescale thermostat and the Parinello-Rahman barostat. Is there any
>> particular reason for this choice? Would you please provide any reference
>> that is combinantion works well in comparison to others or its just the
>> example?
>>
>>
> The original references for each of the algorithms prove that they
> adequately sample the desired ensembles.  For the purposes of tutorials,
> these algorithms are robust, and I avoid Berendsen because I experience has
> shown me that people simply assume that whatever is in the tutorial is
> "correct" so I at least attempt to avoid leading people into making
> mistakes.
>
> -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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